Variant report

Variant	rs6727888
Chromosome Location	chr2:62887884-62887885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62886383..62889324-chr2:62914421..62916883,2	K562	blood:
2	chr2:62886240..62888184-chr2:62910280..62913021,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10168771	0.91[EUR][1000 genomes]
rs10172216	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10174703	0.83[ASN][1000 genomes]
rs10177638	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10179232	0.86[ASN][1000 genomes]
rs1038572	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs10496099	0.83[EUR][1000 genomes]
rs11125941	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11682530	0.93[JPT][hapmap]
rs11688816	0.86[JPT][hapmap]
rs11893614	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12328837	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12989754	0.87[JPT][hapmap]
rs13013218	0.81[JPT][hapmap]
rs13397831	0.82[ASN][1000 genomes]
rs13423306	0.86[ASN][1000 genomes]
rs1386399	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1386401	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs1487074	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1527959	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1534418	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1534419	0.95[CEU][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1534420	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553832	0.87[JPT][hapmap]
rs1830260	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1843779	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1872789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1872790	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs189671	0.87[JPT][hapmap]
rs2129509	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2136737	0.87[JPT][hapmap]
rs2204655	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2204656	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2421713	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2901516	0.87[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	0.86[ASN][1000 genomes]
rs4461246	0.87[JPT][hapmap]
rs4479415	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671050	0.93[JPT][hapmap]
rs6545965	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545966	0.81[ASN][1000 genomes]
rs6545967	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545969	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545971	0.86[JPT][hapmap]
rs6705835	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6706506	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6749020	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6752010	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6757128	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7349258	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7421841	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7573756	0.87[JPT][hapmap]
rs9678363	0.86[ASN][1000 genomes]
rs974344	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs974345	0.82[EUR][1000 genomes];0.95[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
rs6727888	CCT4	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62870400-62889600	Weak transcription	Right Atrium	heart
2	chr2:62882000-62892000	Weak transcription	Fetal Intestine Large	intestine
3	chr2:62882400-62888200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:62882400-62890000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:62882600-62888200	Weak transcription	Esophagus	oesophagus
6	chr2:62885200-62889600	Weak transcription	Psoas Muscle	Psoas
7	chr2:62886200-62888400	Enhancers	NHDF-Ad	bronchial
8	chr2:62886200-62888600	Enhancers	Fetal Brain Male	brain
9	chr2:62886400-62890600	Enhancers	NHLF	lung
10	chr2:62886400-62893400	Enhancers	HMEC	breast
11	chr2:62886600-62888200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:62886600-62888600	Enhancers	Fetal Stomach	stomach
13	chr2:62886600-62888800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:62886600-62889000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:62886600-62889800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:62886600-62889800	Weak transcription	Fetal Brain Female	brain
17	chr2:62886600-62892800	Enhancers	Osteobl	bone
18	chr2:62886600-62894000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:62886600-62894200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:62886800-62888000	Enhancers	Primary B cells from cord blood	blood
21	chr2:62886800-62888000	Enhancers	Primary B cells from peripheral blood	blood
22	chr2:62886800-62888400	Enhancers	HSMM	muscle
23	chr2:62886800-62888600	Enhancers	A549	lung
24	chr2:62886800-62888600	Flanking Active TSS	GM12878-XiMat	blood
25	chr2:62886800-62892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:62887000-62888000	Enhancers	Fetal Heart	heart
27	chr2:62887000-62888400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr2:62887000-62888600	Flanking Active TSS	NHEK	skin
29	chr2:62887000-62888800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:62887000-62889000	Enhancers	HSMMtube	muscle
31	chr2:62887000-62889600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:62887200-62888200	Enhancers	NH-A	brain
33	chr2:62887200-62888800	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr2:62887200-62888800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:62887200-62889000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:62887200-62894000	Enhancers	HepG2	liver
37	chr2:62887400-62888000	Weak transcription	Fetal Kidney	kidney
38	chr2:62887400-62888000	Weak transcription	Fetal Lung	lung
39	chr2:62887400-62888400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:62887400-62889000	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr2:62887400-62889600	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:62887400-62894000	Enhancers	Colon Smooth Muscle	Colon
43	chr2:62887400-62899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:62887600-62888000	Weak transcription	Placenta	Placenta
45	chr2:62887600-62888000	Weak transcription	Ovary	ovary
46	chr2:62887600-62888000	Weak transcription	Spleen	Spleen
47	chr2:62887600-62888200	Weak transcription	Adipose Nuclei	Adipose
48	chr2:62887600-62888400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr2:62887600-62888600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:62887600-62889400	Enhancers	Liver	Liver

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