Variant report

Variant	rs3931397
Chromosome Location	chr4:149079497-149079498
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10023128	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10031194	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10519942	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11725360	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11729617	0.85[ASN][1000 genomes]
rs17024404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17024408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs17024437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024443	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17620330	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1879827	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2293162	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs28367185	0.96[ASN][1000 genomes]
rs28368806	1.00[ASN][1000 genomes]
rs28789690	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846299	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57616130	0.96[ASN][1000 genomes]
rs61757920	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62331988	0.86[ASN][1000 genomes]
rs62332226	1.00[ASN][1000 genomes]
rs6535580	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6535581	0.86[JPT][hapmap]
rs6811001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6816503	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7670173	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7670229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032794	chr4:149046598-149135489	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537295	chr4:149046598-149135489	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Corneal structure	23291589	GWAS catalog

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149018000-149085800	Weak transcription	Stomach Mucosa	stomach
2	chr4:149040600-149083200	Weak transcription	Gastric	stomach
3	chr4:149041400-149092000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:149045600-149104800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:149046400-149085800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:149046600-149087400	Weak transcription	Aorta	Aorta
7	chr4:149047400-149083800	Weak transcription	Small Intestine	intestine
8	chr4:149049400-149083000	Weak transcription	Fetal Intestine Large	intestine
9	chr4:149055000-149087400	Weak transcription	Psoas Muscle	Psoas
10	chr4:149063000-149087400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:149063200-149085600	Weak transcription	Fetal Intestine Small	intestine
12	chr4:149067600-149087400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:149068000-149083200	Weak transcription	Left Ventricle	heart
14	chr4:149068000-149085800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:149068000-149085800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:149068000-149097400	Weak transcription	Spleen	Spleen
17	chr4:149068200-149087400	Weak transcription	Esophagus	oesophagus
18	chr4:149069200-149087400	Weak transcription	Adipose Nuclei	Adipose
19	chr4:149069600-149081000	Weak transcription	Pancreas	Pancrea
20	chr4:149073200-149085800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:149073800-149081000	Weak transcription	Fetal Kidney	kidney
22	chr4:149074000-149081200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:149074200-149080400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:149074800-149085800	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:149075000-149083200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:149075800-149081000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:149075800-149084800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:149075800-149085800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:149076000-149082000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:149076000-149083000	Weak transcription	Lung	lung
31	chr4:149076000-149085800	Weak transcription	Ovary	ovary
32	chr4:149076000-149088200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:149076000-149094600	Weak transcription	Fetal Stomach	stomach
34	chr4:149076400-149080600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:149079200-149080000	Enhancers	Pancreatic Islets	Pancreatic Islet

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