Variant report

Variant	rs10177638
Chromosome Location	chr2:62887010-62887011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62886383..62889324-chr2:62914421..62916883,2	K562	blood:
2	chr2:62886240..62888184-chr2:62910280..62913021,2	K562	blood:
3	chr2:62883737..62887558-chr2:62889986..62892467,3	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10168771	0.87[EUR][1000 genomes]
rs10172216	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10174703	0.84[ASN][1000 genomes]
rs10179232	0.88[ASN][1000 genomes]
rs1038572	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs10496099	0.87[EUR][1000 genomes]
rs11125941	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682530	0.93[JPT][hapmap]
rs11688816	0.86[JPT][hapmap]
rs11893614	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12328837	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12989754	0.87[JPT][hapmap]
rs13013218	0.81[JPT][hapmap]
rs13423306	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1386399	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1386401	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs1487074	0.83[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1527959	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1534418	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534419	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534420	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553832	0.87[JPT][hapmap]
rs1830260	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1843779	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1872789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1872790	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs189671	0.87[JPT][hapmap]
rs1997246	0.81[AFR][1000 genomes]
rs2129509	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2136737	0.87[JPT][hapmap]
rs2204655	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2204656	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2421713	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28814605	0.80[ASN][1000 genomes]
rs2901516	0.89[ASN][1000 genomes]
rs360799	0.87[JPT][hapmap]
rs360800	0.87[JPT][hapmap]
rs360801	0.87[JPT][hapmap]
rs360804	0.87[JPT][hapmap]
rs360807	0.93[JPT][hapmap]
rs4449117	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4461246	0.87[JPT][hapmap]
rs4479415	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671050	0.93[JPT][hapmap]
rs6545965	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545966	0.82[ASN][1000 genomes]
rs6545967	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545969	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545971	0.86[JPT][hapmap]
rs6705835	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6706506	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6727888	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749020	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6752010	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6757128	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7349258	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7420881	0.82[ASN][1000 genomes]
rs7421841	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7573756	0.87[JPT][hapmap]
rs9678363	0.89[ASN][1000 genomes]
rs9679110	0.82[ASN][1000 genomes]
rs974344	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs974345	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10177638	CCT4	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62870400-62889600	Weak transcription	Right Atrium	heart
2	chr2:62881800-62887200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:62882000-62892000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:62882200-62887200	Weak transcription	NH-A	brain
5	chr2:62882400-62888200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:62882400-62890000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:62882600-62887200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:62882600-62888200	Weak transcription	Esophagus	oesophagus
9	chr2:62883600-62887200	Weak transcription	HepG2	liver
10	chr2:62885200-62889600	Weak transcription	Psoas Muscle	Psoas
11	chr2:62886000-62887800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:62886200-62888400	Enhancers	NHDF-Ad	bronchial
13	chr2:62886200-62888600	Enhancers	Fetal Brain Male	brain
14	chr2:62886400-62887200	Enhancers	Stomach Smooth Muscle	stomach
15	chr2:62886400-62890600	Enhancers	NHLF	lung
16	chr2:62886400-62893400	Enhancers	HMEC	breast
17	chr2:62886600-62887200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr2:62886600-62887200	Enhancers	Rectal Smooth Muscle	rectum
19	chr2:62886600-62887600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:62886600-62888200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:62886600-62888600	Enhancers	Fetal Stomach	stomach
22	chr2:62886600-62888800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr2:62886600-62889000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:62886600-62889800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:62886600-62889800	Weak transcription	Fetal Brain Female	brain
26	chr2:62886600-62892800	Enhancers	Osteobl	bone
27	chr2:62886600-62894000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:62886600-62894200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:62886800-62887200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr2:62886800-62887400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:62886800-62887600	Enhancers	Placenta	Placenta
32	chr2:62886800-62887600	Enhancers	Ovary	ovary
33	chr2:62886800-62888000	Enhancers	Primary B cells from cord blood	blood
34	chr2:62886800-62888000	Enhancers	Primary B cells from peripheral blood	blood
35	chr2:62886800-62888400	Enhancers	HSMM	muscle
36	chr2:62886800-62888600	Enhancers	A549	lung
37	chr2:62886800-62888600	Flanking Active TSS	GM12878-XiMat	blood
38	chr2:62886800-62892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:62887000-62887400	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr2:62887000-62887600	Flanking Active TSS	Liver	Liver
41	chr2:62887000-62888000	Enhancers	Fetal Heart	heart
42	chr2:62887000-62888400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr2:62887000-62888600	Flanking Active TSS	NHEK	skin
44	chr2:62887000-62888800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:62887000-62889000	Enhancers	HSMMtube	muscle
46	chr2:62887000-62889600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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