Variant report

Variant	rs3777478
Chromosome Location	chr6:131535042-131535043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10484765	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12203075	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1358962	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1407532	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1407533	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1729551	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1885640	0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2146827	0.82[ASN][1000 genomes]
rs3777480	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777483	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777494	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3822866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3850238	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4311533	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4327722	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4484548	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897505	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66827112	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6922252	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6924196	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7744734	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7754788	0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7755640	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7761587	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7768335	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9321277	0.86[ASN][1000 genomes]
rs9375806	0.85[ASN][1000 genomes]
rs9398980	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9483237	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9483239	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9483244	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9483245	0.85[AMR][1000 genomes]
rs9492886	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv886665	chr6:131518894-131611309	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv830808	chr6:131521115-131735320	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3777478	VNN1	cis	cerebellum	SCAN
rs3777478	AKAP7	cis	parietal	SCAN
rs3777478	TAAR9	cis	parietal	SCAN
rs3777478	TCF21	cis	cerebellum	SCAN
rs3777478	SNORD101	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131506800-131551800	Weak transcription	Ovary	ovary
2	chr6:131513200-131536400	Weak transcription	Esophagus	oesophagus
3	chr6:131514400-131541400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:131521200-131536200	Weak transcription	Lung	lung
5	chr6:131521200-131541400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:131521600-131535200	Weak transcription	Right Ventricle	heart
7	chr6:131521600-131537400	Weak transcription	Adipose Nuclei	Adipose
8	chr6:131522400-131542200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:131522400-131542200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:131528000-131541400	Weak transcription	Primary B cells from cord blood	blood
11	chr6:131528000-131544800	Weak transcription	Fetal Brain Male	brain
12	chr6:131532200-131537000	Weak transcription	Liver	Liver
13	chr6:131532400-131541200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:131533000-131535400	Enhancers	Fetal Lung	lung
15	chr6:131533200-131535400	Enhancers	Fetal Stomach	stomach
16	chr6:131533200-131537600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:131533600-131535400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:131533600-131535400	Enhancers	Fetal Intestine Large	intestine
19	chr6:131533600-131535600	Enhancers	Fetal Intestine Small	intestine
20	chr6:131533600-131538000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:131533800-131535400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:131533800-131537400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:131534000-131535200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:131534000-131535600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:131534000-131537800	Enhancers	Primary T cells from cord blood	blood
26	chr6:131534200-131536400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:131534200-131536600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:131534200-131536600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:131534400-131535400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:131534400-131535600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:131534600-131535200	Enhancers	Primary hematopoietic stem cells	blood
32	chr6:131534600-131535200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr6:131534600-131535200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:131534600-131535200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:131534600-131535200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:131534600-131535200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:131534600-131535200	Enhancers	Brain Anterior Caudate	brain
38	chr6:131534600-131535200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr6:131534600-131535200	Enhancers	Fetal Kidney	kidney
40	chr6:131534600-131535200	Flanking Active TSS	Dnd41	blood
41	chr6:131534600-131535400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr6:131534600-131535400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:131534600-131535400	Enhancers	Primary T cells fromperipheralblood	blood
44	chr6:131534600-131535400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:131534600-131535400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:131534600-131535400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:131534600-131535400	Enhancers	Brain Hippocampus Middle	brain
48	chr6:131534600-131535400	Enhancers	Fetal Thymus	thymus
49	chr6:131534600-131535600	Enhancers	Brain Substantia Nigra	brain
50	chr6:131534600-131536000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links