Variant report

Variant	rs661126
Chromosome Location	chr1:93678968-93678969
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1010476	0.85[CHD][hapmap]
rs1060622	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10782959	0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs11164870	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11164876	0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs11164879	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11164908	0.82[CHB][hapmap]
rs12030549	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12030843	0.82[CHB][hapmap]
rs12033147	0.80[CHB][hapmap]
rs12038699	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs12044557	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs12044883	0.90[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12118262	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12128131	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12133576	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs12138486	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs12139009	0.83[AMR][1000 genomes]
rs12139633	0.81[AFR][1000 genomes]
rs12406245	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12563120	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs1335679	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs1426318	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1474927	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs1535701	0.88[AFR][1000 genomes]
rs1559828	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs1572343	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs1856027	0.91[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs1932314	1.00[YRI][hapmap]
rs2031225	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2031226	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2255722	0.88[CHD][hapmap]
rs2281524	0.83[CHD][hapmap]
rs2295423	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2295424	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2296558	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2391254	0.87[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2484486	0.85[CHD][hapmap]
rs2749732	0.83[CHD][hapmap]
rs2765545	0.87[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap]
rs2783489	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap]
rs2783490	0.88[CHD][hapmap]
rs2783495	0.88[CHD][hapmap]
rs2783499	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs2783500	0.81[CHB][hapmap]
rs2783501	0.82[CHB][hapmap]
rs2815429	0.83[CHD][hapmap]
rs3754186	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3767964	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3904666	0.88[CHD][hapmap]
rs4000699	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4240966	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs4484937	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs4847235	0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs4847240	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs4847398	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4847399	0.90[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes]
rs4847408	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs531358	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs547866	0.81[AFR][1000 genomes]
rs565919	0.80[AFR][1000 genomes]
rs569414	0.90[CEU][hapmap]
rs612037	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs622608	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs624131	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs637646	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6541349	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs6541401	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6541404	0.83[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs6682670	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs6703310	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs687394	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs693737	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs7513705	0.87[CEU][hapmap];0.91[CHB][hapmap]
rs7517363	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7525248	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7535628	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs7539307	0.87[CEU][hapmap];0.91[CHB][hapmap]
rs7553916	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs771481	0.86[CHB][hapmap]
rs797661	0.80[ASN][1000 genomes]
rs797668	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs797675	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs797676	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs797680	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs810027	0.88[CHD][hapmap]
rs942196	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]

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	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs661126	GCLM	cis	cerebellum	SCAN
rs661126	F3	cis	cerebellum	SCAN
rs661126	CCDC18	cis	parietal	SCAN
rs661126	DR1	cis	multi-tissue	Pritchard
rs661126	TMED5	cis	cerebellum	SCAN
rs661126	TMED5	cis	parietal	SCAN
rs661126	BARHL2	cis	parietal	SCAN
rs661126	DR1	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93688000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:93647000-93688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:93647000-93756400	Weak transcription	Gastric	stomach
4	chr1:93647200-93681200	Weak transcription	HUVEC	blood vessel
5	chr1:93647200-93684400	Weak transcription	NH-A	brain
6	chr1:93647200-93685000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:93647600-93706600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:93649000-93684800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:93651000-93684800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:93654200-93708400	Weak transcription	Esophagus	oesophagus
13	chr1:93654600-93708000	Weak transcription	Ovary	ovary
14	chr1:93656400-93686200	Weak transcription	Aorta	Aorta
15	chr1:93657000-93682000	Strong transcription	Dnd41	blood
16	chr1:93657600-93708400	Weak transcription	Left Ventricle	heart
17	chr1:93658600-93684800	Weak transcription	Primary T cells from cord blood	blood
18	chr1:93658800-93684400	Weak transcription	Osteobl	bone
19	chr1:93660600-93705200	Weak transcription	Lung	lung
20	chr1:93660800-93685000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:93661400-93708200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:93661800-93702800	Weak transcription	Fetal Heart	heart
23	chr1:93661800-93708200	Weak transcription	Fetal Brain Female	brain
24	chr1:93663600-93705600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:93665400-93684200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:93665400-93684400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:93665400-93685000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:93665400-93688800	Weak transcription	NHLF	lung
29	chr1:93665400-93708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:93665400-93708400	Weak transcription	Spleen	Spleen
31	chr1:93665600-93683000	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:93665600-93697600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:93665600-93702600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:93665600-93707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:93665800-93684200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:93665800-93684400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:93665800-93693200	Weak transcription	Fetal Intestine Small	intestine
38	chr1:93665800-93706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:93665800-93707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:93666200-93684200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:93667400-93687600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:93667400-93695400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:93668000-93683600	Weak transcription	Adipose Nuclei	Adipose
45	chr1:93668600-93683400	Weak transcription	NHDF-Ad	bronchial
46	chr1:93668600-93684200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:93668800-93685200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:93668800-93686000	Weak transcription	Fetal Lung	lung
49	chr1:93668800-93695200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:93668800-93697600	Weak transcription	Fetal Intestine Large	intestine

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