Variant report

Variant	rs829626
Chromosome Location	chr2:30756528-30756529
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10197664	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205934	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10495776	0.91[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1096110	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11127276	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1113661	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11676852	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11678346	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1252644	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12612080	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616814	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12621663	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714308	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1464817	0.87[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1807334	0.82[LWK][hapmap];0.88[YRI][hapmap]
rs2363073	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593432	0.87[CEU][hapmap];0.92[JPT][hapmap]
rs2593438	0.87[CEU][hapmap];0.93[JPT][hapmap]
rs2593446	0.87[YRI][hapmap]
rs2609927	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2609944	0.82[LWK][hapmap];0.88[YRI][hapmap]
rs36072623	0.80[AMR][1000 genomes]
rs6712951	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6718730	0.81[JPT][hapmap]
rs711242	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71412838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736256	0.91[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs7602714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829668	0.92[EUR][1000 genomes]
rs9789517	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs829626	GCKR	cis	parietal	SCAN
rs829626	EMILIN1	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30729000-30764600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:30734800-30764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:30738000-30757000	Weak transcription	Ovary	ovary
4	chr2:30738200-30758200	Weak transcription	Right Ventricle	heart
5	chr2:30743000-30757000	Weak transcription	Left Ventricle	heart
6	chr2:30743000-30758200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:30743000-30758200	Weak transcription	Pancreas	Pancrea
8	chr2:30743000-30758400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:30743000-30758600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:30743000-30759000	Weak transcription	Gastric	stomach
11	chr2:30743000-30759800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:30743000-30759800	Weak transcription	Esophagus	oesophagus
13	chr2:30743000-30761000	Weak transcription	NHEK	skin
14	chr2:30743000-30763600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:30743000-30764600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:30743000-30764600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:30743000-30767400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:30743000-30768000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:30743200-30757000	Weak transcription	Fetal Stomach	stomach
20	chr2:30743200-30757000	Weak transcription	Lung	lung
21	chr2:30743200-30757400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:30743200-30760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:30746000-30757600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:30746400-30757200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:30746400-30758200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:30748200-30757600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:30748800-30757400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:30748800-30758200	Weak transcription	Fetal Brain Male	brain
29	chr2:30749000-30757000	Weak transcription	Fetal Intestine Small	intestine
30	chr2:30749000-30757400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:30749000-30757600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:30749000-30758000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:30749000-30758000	Weak transcription	Fetal Lung	lung
34	chr2:30749000-30812600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:30749200-30758200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:30749600-30758600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:30749600-30759000	Weak transcription	Fetal Brain Female	brain
38	chr2:30749800-30757600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:30750200-30757800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:30750400-30759600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:30750400-30760000	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:30751000-30758200	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:30751000-30760800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:30751000-30766800	Weak transcription	NHLF	lung
45	chr2:30751200-30758200	Weak transcription	NHDF-Ad	bronchial
46	chr2:30751400-30756600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:30751400-30759800	Weak transcription	Osteobl	bone
48	chr2:30752600-30758200	Weak transcription	Aorta	Aorta
49	chr2:30752800-30757800	Weak transcription	Brain Anterior Caudate	brain
50	chr2:30752800-30758200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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