Variant report

Variant	rs2481676
Chromosome Location	chr1:62627675-62627676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11804701	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs17123137	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs17123151	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs17569387	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs2476194	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012683	chr1:62587852-62643998	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2481676	INADL	cis	cerebellum	SCAN
rs2481676	RAVER2	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
4	chr1:62605000-62631800	Weak transcription	Lung	lung
5	chr1:62606400-62628600	Weak transcription	Stomach Mucosa	stomach
6	chr1:62607000-62630000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:62608400-62643600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:62612400-62629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:62612400-62632600	Weak transcription	Brain Angular Gyrus	brain
10	chr1:62613400-62636000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:62614400-62628400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:62614400-62628800	Weak transcription	Ovary	ovary
13	chr1:62615200-62629000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:62615200-62629400	Weak transcription	NHEK	skin
15	chr1:62616200-62628200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:62616200-62629400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:62616200-62631800	Weak transcription	Right Ventricle	heart
18	chr1:62617200-62632000	Weak transcription	HMEC	breast
19	chr1:62617800-62631600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:62618000-62628800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:62618200-62629200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:62618200-62629600	Weak transcription	Primary T cells from cord blood	blood
23	chr1:62618200-62629800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:62618400-62629400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:62618600-62629200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:62618600-62631400	Weak transcription	Gastric	stomach
27	chr1:62618600-62631800	Weak transcription	Pancreas	Pancrea
28	chr1:62618600-62637800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:62621000-62631000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:62621000-62632600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:62621200-62628600	Weak transcription	Esophagus	oesophagus
32	chr1:62621200-62631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:62621200-62636600	Weak transcription	Fetal Intestine Large	intestine
34	chr1:62622600-62638000	Weak transcription	Fetal Intestine Small	intestine
35	chr1:62625200-62631000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:62625600-62628200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:62625600-62628200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr1:62626000-62628200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:62626400-62628200	Strong transcription	Liver	Liver
40	chr1:62626600-62628200	Strong transcription	Aorta	Aorta
41	chr1:62626600-62628200	Strong transcription	Left Ventricle	heart
42	chr1:62627000-62642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:62627200-62628200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:62627200-62628400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:62627400-62628400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:62627600-62629200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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