Variant report

Variant	rs499083
Chromosome Location	chr19:56623710-56623711
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56621941..56623782-chr19:56652294..56654418,2	MCF-7	breast:
2	chr19:56600362..56602994-chr19:56622256..56625120,2	K562	blood:
3	chr19:56599644..56602994-chr19:56620278..56624249,5	K562	blood:
4	chr19:56622447..56624561-chr19:56624820..56626389,2	MCF-7	breast:
5	chr19:56606614..56610711-chr19:56622862..56625649,3	MCF-7	breast:
6	chr19:56622659..56624713-chr19:56687287..56689653,2	K562	blood:
7	chr19:56601293..56604131-chr19:56623089..56625582,2	MCF-7	breast:
8	chr19:56622071..56628058-chr19:56628441..56634693,11	MCF-7	breast:
9	chr19:56622267..56625662-chr19:56649555..56652513,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000142409	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000197487	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10409172	1.00[JPT][hapmap]
rs11673628	0.89[CEU][hapmap]
rs12983086	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs28553904	1.00[JPT][hapmap]
rs473045	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801676	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs490015	0.88[ASN][1000 genomes]
rs496526	0.94[ASN][1000 genomes]
rs506986	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs511610	0.88[ASN][1000 genomes]
rs511642	0.88[ASN][1000 genomes]
rs529291	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs562907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs629836	1.00[ASN][1000 genomes]
rs672824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs9676765	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer 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	41 gene(s)	inside rSNPs	diseases
6	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
16	esv1809307	chr19:56604027-56633623	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv1811581	chr19:56609313-56631618	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
18	esv1824038	chr19:56610449-56636632	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:56616000-56626600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr19:56616000-56627000	Enhancers	Liver	Liver
4	chr19:56616000-56627200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr19:56617200-56624400	Weak transcription	Hela-S3	cervix
6	chr19:56617200-56629200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:56618200-56624400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:56618600-56630000	Weak transcription	Dnd41	blood
9	chr19:56618800-56626400	Enhancers	Fetal Thymus	thymus
10	chr19:56619200-56624200	Enhancers	Placenta	Placenta
11	chr19:56619200-56627200	Enhancers	Left Ventricle	heart
12	chr19:56619600-56625000	Enhancers	Fetal Heart	heart
13	chr19:56619600-56627200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:56619800-56623800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:56619800-56624800	Enhancers	Fetal Intestine Large	intestine
16	chr19:56619800-56625400	Enhancers	Fetal Lung	lung
17	chr19:56620000-56627000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr19:56620200-56625000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr19:56620400-56625400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr19:56620400-56631000	Enhancers	Pancreas	Pancrea
21	chr19:56620600-56623800	Weak transcription	Fetal Brain Female	brain
22	chr19:56620600-56625000	Enhancers	Stomach Mucosa	stomach
23	chr19:56620800-56625800	Enhancers	Brain Hippocampus Middle	brain
24	chr19:56620800-56626200	Enhancers	Fetal Muscle Leg	muscle
25	chr19:56620800-56627200	Enhancers	Right Atrium	heart
26	chr19:56620800-56630400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr19:56620800-56631000	Weak transcription	Aorta	Aorta
28	chr19:56621000-56626000	Weak transcription	NHEK	skin
29	chr19:56621000-56630000	Weak transcription	NHDF-Ad	bronchial
30	chr19:56621400-56625400	Enhancers	HUVEC	blood vessel
31	chr19:56621600-56625000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr19:56621600-56625000	Enhancers	HSMM	muscle
33	chr19:56621600-56625200	Enhancers	Brain Substantia Nigra	brain
34	chr19:56621600-56626600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:56621600-56626600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:56621600-56626800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr19:56621800-56624000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr19:56621800-56624800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:56621800-56624800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr19:56621800-56625000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:56621800-56625000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:56621800-56626400	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr19:56621800-56626600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr19:56622000-56623800	Enhancers	Placenta Amnion	Placenta Amnion
45	chr19:56622000-56623800	Flanking Active TSS	GM12878-XiMat	blood
46	chr19:56622000-56624200	Genic enhancers	A549	lung
47	chr19:56622000-56624600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:56622000-56625000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:56622000-56625000	Weak transcription	Fetal Kidney	kidney
50	chr19:56622000-56625000	Genic enhancers	Fetal Stomach	stomach

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