Variant report

Variant	rs7960380
Chromosome Location	chr12:31714251-31714252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31711892..31714332-chr12:31715777..31718020,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10771826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10771830	0.84[EUR][1000 genomes]
rs10771831	0.81[EUR][1000 genomes]
rs10771833	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10771834	0.81[EUR][1000 genomes]
rs10771835	0.87[EUR][1000 genomes]
rs10771837	0.86[EUR][1000 genomes]
rs10843937	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs10843938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs10843939	0.81[EUR][1000 genomes]
rs10843953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs10843954	0.86[EUR][1000 genomes]
rs10843957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843962	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843966	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843968	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843971	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843972	0.89[EUR][1000 genomes]
rs11051417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11051427	0.82[EUR][1000 genomes]
rs11051428	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11051440	0.90[EUR][1000 genomes]
rs11051446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11051454	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051461	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11051467	0.96[CEU][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051472	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051476	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11051478	0.83[EUR][1000 genomes]
rs1150949	0.87[ASN][1000 genomes]
rs12368987	0.89[EUR][1000 genomes]
rs12369701	0.91[ASN][1000 genomes]
rs12371432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1259360	0.87[ASN][1000 genomes]
rs1268747	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1677193	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs16918740	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879385	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2163730	0.82[EUR][1000 genomes]
rs2351921	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2351922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2351923	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34498192	0.85[EUR][1000 genomes]
rs3741877	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs3741878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3803114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3850966	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887250	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3898712	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4930979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4931499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs4931511	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4931512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4931513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61097018	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61918606	0.81[EUR][1000 genomes]
rs6487991	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6487995	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7136559	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7297507	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297997	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7300106	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs7301326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7302695	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73080572	0.82[EUR][1000 genomes]
rs7308202	0.84[EUR][1000 genomes]
rs7311970	0.90[EUR][1000 genomes]
rs7313889	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs7314404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs7314739	0.81[EUR][1000 genomes]
rs7963764	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7980274	0.83[EUR][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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7960380	ERGIC2	cis	cerebellum	SCAN
rs7960380	DENND5B	cis	cerebellum	SCAN
rs7960380	YARS2	cis	cerebellum	SCAN
rs7960380	DENND5B	cis	parietal	SCAN
rs7960380	FLJ13224	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31696200-31722400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:31709200-31727600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:31709400-31722600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:31710000-31714600	Weak transcription	A549	lung
5	chr12:31710200-31723800	Weak transcription	Pancreas	Pancrea
6	chr12:31711000-31727400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:31712200-31721000	Weak transcription	Primary B cells from cord blood	blood
8	chr12:31712200-31723600	Weak transcription	NH-A	brain
9	chr12:31712800-31714400	Enhancers	HepG2	liver
10	chr12:31713000-31714400	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:31713000-31715200	ZNF genes & repeats	GM12878-XiMat	blood
12	chr12:31713200-31714400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:31713600-31714400	Enhancers	Ovary	ovary
14	chr12:31713600-31720800	Weak transcription	Aorta	Aorta
15	chr12:31713800-31720200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:31714000-31716000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:31714000-31721400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:31714200-31715800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:31714200-31716000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:31714200-31716000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:31714200-31716000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:31714200-31726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:31714200-31728600	Weak transcription	Psoas Muscle	Psoas

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