Variant report

Variant	rs9900054
Chromosome Location	chr17:17414839-17414840
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:17414740-17414890	GM12864	blood:	n/a	n/a
2	CTCF	chr17:17414720-17414870	HAc	cerebellar:	n/a	chr17:17414739-17414757
3	SPI1	chr17:17414534-17414895	HL-60	blood:	n/a	chr17:17414593-17414606
4	CTCF	chr17:17414720-17414870	AG04449	skin:	n/a	chr17:17414739-17414757
5	CTCF	chr17:17414760-17414910	HRE	kidney:	n/a	n/a
6	CTCF	chr17:17414700-17414850	NB4	blood:	n/a	chr17:17414739-17414757
7	CTCF	chr17:17414700-17414850	WERI-Rb-1	eye:	n/a	chr17:17414739-17414757

No.	Distal block	Cell Line	Cell type
1	chr17:17412469..17415269-chr17:17430447..17432803,2	MCF-7	breast:
2	chr17:17414329..17416478-chr17:17418151..17420327,2	K562	blood:
3	chr17:17402799..17405333-chr17:17413416..17415879,2	K562	blood:
4	chr17:17413540..17416682-chr17:17491858..17494964,3	MCF-7	breast:

Variant related genes	Relation type
PEMT	TF binding region
ENSG00000264666	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12103816	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12103822	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs3744120	1.00[EUR][1000 genomes]
rs4646353	1.00[EUR][1000 genomes]
rs4646373	1.00[EUR][1000 genomes]
rs4646374	1.00[EUR][1000 genomes]
rs4646375	1.00[EUR][1000 genomes]
rs4646378	1.00[EUR][1000 genomes]
rs4646382	1.00[EUR][1000 genomes]
rs4646384	1.00[EUR][1000 genomes]
rs4646386	1.00[EUR][1000 genomes]
rs56046764	1.00[EUR][1000 genomes]
rs58990997	1.00[EUR][1000 genomes]
rs58992576	1.00[EUR][1000 genomes]
rs61692723	1.00[EUR][1000 genomes]
rs70963024	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73978955	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73978967	1.00[EUR][1000 genomes]
rs73978971	1.00[EUR][1000 genomes]
rs73978975	1.00[EUR][1000 genomes]
rs8076828	1.00[EUR][1000 genomes]
rs879375	1.00[EUR][1000 genomes]
rs9902188	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv907730	chr17:17358004-17415217	Strong transcription Genic enhancers Weak transcription Enhancers 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 target site	18 gene(s)	inside rSNPs	diseases
4	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv907732	chr17:17381764-17415217	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv907733	chr17:17381764-17422608	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv907734	chr17:17381764-17425858	Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv907735	chr17:17381764-17448589	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv907738	chr17:17404586-17422608	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv907739	chr17:17404586-17424333	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv907740	chr17:17404586-17425858	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv907741	chr17:17404586-17429927	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv907742	chr17:17404586-17432744	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv907743	chr17:17404586-17448589	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 target site	12 gene(s)	inside rSNPs	diseases
17	esv1803680	chr17:17408484-17426009	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
18	nsv574525	chr17:17411030-17422608	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv907745	chr17:17411211-17429927	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv907746	chr17:17412032-17478917	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17400600-17415200	Weak transcription	Ovary	ovary
2	chr17:17400600-17422000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:17400800-17419200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr17:17401000-17418800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:17401000-17425400	Weak transcription	Thymus	Thymus
6	chr17:17401200-17415200	Weak transcription	Gastric	stomach
7	chr17:17406200-17415800	Enhancers	Fetal Heart	heart
8	chr17:17407400-17425400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr17:17407800-17418400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr17:17407800-17422600	Weak transcription	Brain Germinal Matrix	brain
11	chr17:17408000-17418200	Weak transcription	Fetal Brain Female	brain
12	chr17:17408000-17418400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:17408200-17419200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr17:17408400-17417600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr17:17410200-17418200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:17410200-17426400	Weak transcription	Fetal Intestine Large	intestine
17	chr17:17410400-17415400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:17410800-17415200	Weak transcription	Esophagus	oesophagus
19	chr17:17411000-17418400	Strong transcription	Fetal Intestine Small	intestine
20	chr17:17411000-17420000	Weak transcription	Pancreas	Pancrea
21	chr17:17411000-17428600	Weak transcription	Brain Hippocampus Middle	brain
22	chr17:17411000-17428600	Weak transcription	Right Atrium	heart
23	chr17:17411000-17428800	Weak transcription	Brain Anterior Caudate	brain
24	chr17:17411400-17417200	Weak transcription	Spleen	Spleen
25	chr17:17411400-17419200	Weak transcription	Right Ventricle	heart
26	chr17:17411400-17423000	Weak transcription	Lung	lung
27	chr17:17411400-17428600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr17:17411600-17425600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr17:17411800-17416600	Enhancers	Fetal Thymus	thymus
30	chr17:17412000-17418200	Weak transcription	Fetal Brain Male	brain
31	chr17:17412200-17415000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:17412400-17416200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:17412800-17415200	Weak transcription	HSMMtube	muscle
34	chr17:17413000-17416200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr17:17413200-17415800	Enhancers	A549	lung
36	chr17:17413200-17416200	Enhancers	Fetal Muscle Leg	muscle
37	chr17:17413200-17437400	Weak transcription	Aorta	Aorta
38	chr17:17413600-17415400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:17413800-17415000	Enhancers	Dnd41	blood
40	chr17:17413800-17415800	Enhancers	Adipose Nuclei	Adipose
41	chr17:17413800-17416200	Enhancers	Primary hematopoietic stem cells	blood
42	chr17:17413800-17416400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr17:17413800-17416400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr17:17413800-17416600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr17:17413800-17416600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr17:17413800-17416600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:17414000-17415000	Weak transcription	K562	blood
48	chr17:17414000-17424000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr17:17414200-17415000	Weak transcription	Liver	Liver
50	chr17:17414200-17415400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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