Variant report

Variant	rs6712274
Chromosome Location	chr2:39627455-39627456
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39626974..39629375-chr2:39635445..39637433,2	MCF-7	breast:
2	chr2:39625232..39628414-chr2:39637317..39639794,4	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10153665	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10170424	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10170617	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10172736	0.82[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs10173556	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10173722	0.83[AFR][1000 genomes]
rs10174268	0.86[CHB][hapmap]
rs10175038	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10190069	0.83[EUR][1000 genomes]
rs10195629	0.83[EUR][1000 genomes]
rs1035232	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10865149	0.88[EUR][1000 genomes]
rs10865150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs10865152	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11124668	0.86[EUR][1000 genomes]
rs11124673	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11124676	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11124679	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1125839	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11688728	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1211996	0.85[EUR][1000 genomes]
rs12622941	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12712636	0.80[EUR][1000 genomes]
rs1468902	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1474424	0.93[MKK][hapmap]
rs1548170	0.86[CHB][hapmap]
rs17023837	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1861735	0.90[EUR][1000 genomes]
rs1922827	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2005892	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2160661	0.87[AFR][1000 genomes]
rs2178762	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2193422	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2373527	0.86[CHB][hapmap]
rs2373534	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2373535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2542008	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2888594	0.92[EUR][1000 genomes]
rs2888598	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3755177	0.90[EUR][1000 genomes]
rs3755178	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3770670	0.90[EUR][1000 genomes]
rs3770675	0.85[EUR][1000 genomes]
rs3770678	0.86[EUR][1000 genomes]
rs3815594	0.84[MEX][hapmap]
rs3887311	0.83[AMR][1000 genomes]
rs4670285	0.83[MEX][hapmap]
rs4670934	0.91[MKK][hapmap]
rs6544210	0.82[CHB][hapmap]
rs6544213	0.86[EUR][1000 genomes]
rs6544220	0.82[EUR][1000 genomes]
rs6544222	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544223	0.93[MKK][hapmap]
rs6544224	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6712921	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6718134	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6725938	0.86[EUR][1000 genomes]
rs6732611	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6736700	0.85[EUR][1000 genomes]
rs6741019	0.86[EUR][1000 genomes]
rs6742170	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6743041	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6753323	0.90[EUR][1000 genomes]
rs6756183	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs6760382	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72801478	0.87[ASN][1000 genomes]
rs7562981	0.86[CHB][hapmap]
rs7569834	0.86[CHB][hapmap]
rs7574250	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7578136	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7579414	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7582160	0.95[MKK][hapmap]
rs759589	0.88[EUR][1000 genomes]
rs7600014	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7600046	0.90[EUR][1000 genomes]
rs7601700	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7603337	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7604047	0.80[EUR][1000 genomes]
rs7608153	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak 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	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	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
rs6712274	COCH	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
3	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:39614000-39628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:39617800-39628200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:39617800-39628400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:39617800-39630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:39618000-39633400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:39619200-39629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:39620000-39629400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:39620200-39635600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:39621800-39628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:39622000-39628200	Weak transcription	Right Ventricle	heart
15	chr2:39622000-39628600	Weak transcription	Lung	lung
16	chr2:39622000-39635400	Weak transcription	HSMM	muscle
17	chr2:39622600-39643600	Weak transcription	Brain Germinal Matrix	brain
18	chr2:39622800-39630400	Weak transcription	Liver	Liver
19	chr2:39622800-39630400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:39622800-39630600	Weak transcription	Fetal Stomach	stomach
21	chr2:39622800-39643200	Weak transcription	Fetal Brain Male	brain
22	chr2:39622800-39643400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:39623600-39628200	Weak transcription	Ovary	ovary
24	chr2:39625200-39630600	Weak transcription	Fetal Intestine Small	intestine
25	chr2:39625400-39630600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:39625400-39634400	Weak transcription	Fetal Intestine Large	intestine
27	chr2:39625800-39627600	Enhancers	Colon Smooth Muscle	Colon
28	chr2:39626000-39629600	Enhancers	HepG2	liver
29	chr2:39626200-39627600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr2:39626200-39627600	Enhancers	Brain Anterior Caudate	brain
31	chr2:39626200-39627800	Enhancers	Fetal Heart	heart
32	chr2:39626200-39628200	Enhancers	Stomach Mucosa	stomach
33	chr2:39626200-39629000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr2:39626200-39629000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr2:39626200-39629400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:39626400-39627600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr2:39626400-39627600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:39626400-39627600	Enhancers	Fetal Lung	lung
39	chr2:39626400-39627600	Enhancers	Psoas Muscle	Psoas
40	chr2:39626400-39627600	Enhancers	A549	lung
41	chr2:39626400-39627600	Enhancers	K562	blood
42	chr2:39626400-39628000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:39626400-39628400	Enhancers	Adipose Nuclei	Adipose
44	chr2:39626400-39628800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr2:39626400-39629000	Enhancers	H9 Cell Line	embryonic stem cell
46	chr2:39626400-39629400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr2:39626600-39627800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr2:39626600-39628400	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr2:39626600-39628600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:39626600-39628600	Enhancers	NHLF	lung

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