Variant report

Variant	rs9899532
Chromosome Location	chr17:43484987-43484988
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:43482138..43486060-chr17:43487634..43490567,4	K562	blood:
2	chr17:43224547..43227139-chr17:43483437..43486269,3	K562	blood:
3	chr17:43224692..43227139-chr17:43483437..43485288,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLEKHM1-2	chr17:43484899-43487751	NONHSAT054116

Variant related genes	Relation type
ENSG00000186834	Chromatin interaction
ENSG00000159314	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs28404811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28432011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28625271	1.00[AMR][1000 genomes]
rs28829290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3859267	1.00[AMR][1000 genomes]
rs56306004	1.00[AMR][1000 genomes]
rs7216519	1.00[AMR][1000 genomes]
rs73986104	1.00[AMR][1000 genomes]
rs73986115	1.00[AMR][1000 genomes]
rs73986136	1.00[AMR][1000 genomes]
rs73986140	1.00[AMR][1000 genomes]
rs73986142	1.00[AMR][1000 genomes]
rs73986145	1.00[AMR][1000 genomes]
rs8075115	1.00[AMR][1000 genomes]
rs8080660	1.00[AMR][1000 genomes]
rs9890871	1.00[AMR][1000 genomes]
rs9891987	1.00[AMR][1000 genomes]
rs9894933	1.00[AMR][1000 genomes]
rs9901147	1.00[AMR][1000 genomes]
rs9905112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9911877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9913023	1.00[AMR][1000 genomes]
rs9914490	1.00[AMR][1000 genomes]
rs9916694	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431632	chr17:43199763-43733983	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	210 gene(s)	inside rSNPs	diseases
2	nsv431633	chr17:43199763-43772540	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	210 gene(s)	inside rSNPs	diseases
3	nsv431634	chr17:43346980-43659975	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv482844	chr17:43361648-43488185	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv427997	chr17:43361649-43488185	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv431636	chr17:43403005-43659881	Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2754858	chr17:43403005-43666906	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	nsv431637	chr17:43403005-43716885	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv428342	chr17:43443554-43651084	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	esv2757659	chr17:43457886-43733983	Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv2758691	chr17:43457886-43816023	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	esv2755280	chr17:43459697-43666906	Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv908304	chr17:43467025-43524511	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1065930	chr17:43467291-44151468	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
15	nsv431638	chr17:43470156-43693538	Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
16	esv2755741	chr17:43470760-43655688	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
17	nsv431639	chr17:43470760-43659355	Bivalent Enhancer Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
18	esv2754089	chr17:43470760-43659881	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	esv34266	chr17:43470760-43659975	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
20	esv34577	chr17:43470760-43659975	Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
21	esv2752564	chr17:43470760-43659975	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
22	esv2753343	chr17:43470760-43659975	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
23	esv2753852	chr17:43470760-43659975	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
24	esv2754692	chr17:43470760-43659975	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
25	esv2754773	chr17:43470760-43659975	Strong transcription Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
26	esv2754821	chr17:43470760-43659975	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
27	esv2755261	chr17:43470760-43659975	Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
28	esv2755434	chr17:43470760-43659975	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
29	esv2755618	chr17:43470760-43659975	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
30	esv2756206	chr17:43470760-43659975	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
31	esv2756211	chr17:43470760-43659975	Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
32	esv2756238	chr17:43470760-43659975	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
33	esv2756640	chr17:43470760-43659975	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
34	esv34307	chr17:43470760-43666906	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
35	esv2755466	chr17:43470760-43666906	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
36	esv2756448	chr17:43470760-43666906	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
37	nsv431640	chr17:43470760-43666906	Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
38	esv2753768	chr17:43470760-43734304	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
39	esv2754725	chr17:43470760-43741452	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:43472600-43485600	Weak transcription	HSMMtube	muscle
2	chr17:43472800-43487400	Weak transcription	HUVEC	blood vessel
3	chr17:43475800-43490400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:43479400-43489600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:43481600-43485400	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr17:43482200-43486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:43482200-43486800	Weak transcription	Liver	Liver
8	chr17:43482200-43487200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:43482400-43485400	Weak transcription	Small Intestine	intestine
10	chr17:43482400-43485600	Weak transcription	Brain Angular Gyrus	brain
11	chr17:43482400-43486400	Weak transcription	Brain Anterior Caudate	brain
12	chr17:43482400-43486600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr17:43482400-43486600	Weak transcription	NHEK	skin
14	chr17:43482400-43487000	Weak transcription	Pancreas	Pancrea
15	chr17:43482400-43501600	Weak transcription	HMEC	breast
16	chr17:43482600-43486600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:43482800-43486200	Weak transcription	K562	blood
18	chr17:43483200-43485400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr17:43483200-43485400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:43483200-43485600	Enhancers	Primary hematopoietic stem cells	blood
21	chr17:43483200-43485600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:43483200-43496000	Weak transcription	Hela-S3	cervix
23	chr17:43483400-43485200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr17:43483400-43485400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr17:43483400-43485600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr17:43483400-43485600	Weak transcription	Right Ventricle	heart
27	chr17:43483400-43485800	Weak transcription	Esophagus	oesophagus
28	chr17:43483400-43486200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:43483400-43486600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr17:43483400-43487000	Weak transcription	Colon Smooth Muscle	Colon
31	chr17:43483400-43487200	Enhancers	Stomach Mucosa	stomach
32	chr17:43483400-43488800	Weak transcription	Psoas Muscle	Psoas
33	chr17:43483600-43485400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:43483600-43485600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr17:43483600-43485600	Genic enhancers	Fetal Thymus	thymus
36	chr17:43483600-43485800	Weak transcription	Brain Substantia Nigra	brain
37	chr17:43483800-43485000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr17:43483800-43485600	Enhancers	Colonic Mucosa	Colon
39	chr17:43483800-43485600	Weak transcription	Fetal Heart	heart
40	chr17:43483800-43485800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr17:43483800-43485800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr17:43483800-43486000	Weak transcription	Gastric	stomach
43	chr17:43483800-43487600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr17:43483800-43488800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr17:43484000-43485200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr17:43484000-43485400	Enhancers	Fetal Intestine Large	intestine
47	chr17:43484000-43485600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr17:43484000-43485600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr17:43484000-43485800	Enhancers	Spleen	Spleen
50	chr17:43484000-43487400	Genic enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links