Variant report

Variant	rs4931536
Chromosome Location	chr12:31817163-31817164
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10843992	0.88[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11051514	0.88[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs11051515	0.88[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11051516	0.88[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11051517	0.87[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs11051519	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051522	0.92[MEX][hapmap]
rs11051527	0.96[ASN][1000 genomes]
rs11051534	0.96[ASN][1000 genomes]
rs11051535	0.98[ASN][1000 genomes]
rs11051536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11051537	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11051538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11051540	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11051546	0.86[ASN][1000 genomes]
rs11051547	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[ASN][1000 genomes]
rs11051549	0.89[AMR][1000 genomes]
rs11051551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes]
rs12231666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4931538	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4931545	0.92[ASN][1000 genomes]
rs4931546	0.95[ASN][1000 genomes]
rs4931547	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59091295	0.88[ASN][1000 genomes]
rs61561194	0.85[ASN][1000 genomes]
rs61932065	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61932089	0.87[AMR][1000 genomes]
rs7308889	0.94[ASN][1000 genomes]
rs7316528	0.85[ASN][1000 genomes]
rs7955365	0.87[ASN][1000 genomes]
rs7959989	0.94[ASN][1000 genomes]

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	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv522379	chr12:31816623-31817163	Weak transcription Enhancers Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4931536	BICD1	cis	cerebellum	SCAN
rs4931536	REP15	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31812800-31818000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:31812800-31818000	Weak transcription	Spleen	Spleen
3	chr12:31812800-31818200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:31812800-31819600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:31812800-31823800	Weak transcription	Small Intestine	intestine
6	chr12:31813000-31817200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:31813000-31822000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:31813000-31822000	Weak transcription	NH-A	brain
9	chr12:31813000-31826000	Weak transcription	Gastric	stomach
10	chr12:31813200-31818000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:31813200-31818000	Weak transcription	Placenta	Placenta
12	chr12:31813200-31818400	Weak transcription	Esophagus	oesophagus
13	chr12:31813200-31822000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:31813200-31837000	Weak transcription	Fetal Brain Male	brain
15	chr12:31813400-31818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:31813400-31820600	Weak transcription	HSMMtube	muscle
17	chr12:31813400-31820800	Weak transcription	Ovary	ovary
18	chr12:31813400-31821600	Weak transcription	Thymus	Thymus
19	chr12:31813400-31821800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:31813400-31821800	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:31813400-31821800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:31813400-31821800	Weak transcription	Fetal Lung	lung
23	chr12:31813400-31822000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:31813400-31822000	Weak transcription	Brain Anterior Caudate	brain
25	chr12:31813400-31822000	Weak transcription	Fetal Intestine Large	intestine
26	chr12:31813400-31822000	Weak transcription	Psoas Muscle	Psoas
27	chr12:31813400-31822000	Weak transcription	Right Ventricle	heart
28	chr12:31813400-31822200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:31813400-31822200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:31813400-31825200	Weak transcription	Aorta	Aorta
31	chr12:31813400-31825400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:31813400-31825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:31813400-31826600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:31813400-31835200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:31813400-31835600	Weak transcription	Brain Angular Gyrus	brain
36	chr12:31813400-31836200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:31813600-31818200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr12:31813600-31821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:31813800-31821800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:31814200-31821800	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:31814200-31821800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:31814800-31817200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:31814800-31817200	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:31815000-31817400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:31815200-31822000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:31815200-31840600	Weak transcription	Pancreas	Pancrea
47	chr12:31815400-31818200	Weak transcription	Fetal Stomach	stomach
48	chr12:31815400-31822200	Weak transcription	Lung	lung
49	chr12:31815600-31821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:31815800-31826200	Weak transcription	Brain Substantia Nigra	brain

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