Variant report

Variant	rs7670939
Chromosome Location	chr4:48703516-48703517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48685998..48688837-chr4:48699802..48703602,5	K562	blood:
2	chr4:48699623..48702132-chr4:48702246..48704804,2	K562	blood:
3	chr4:48699623..48702132-chr4:48702246..48705129,3	K562	blood:
4	chr4:48702489..48705093-chr4:48707646..48709743,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10003273	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10008265	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10010571	0.81[AMR][1000 genomes]
rs10018344	0.80[EUR][1000 genomes]
rs10030853	0.83[EUR][1000 genomes]
rs10031777	0.81[EUR][1000 genomes]
rs10049761	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938534	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs10938537	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs11727343	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap]
rs11728565	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11733534	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs11734019	0.81[EUR][1000 genomes]
rs11737677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11933919	0.83[EUR][1000 genomes]
rs11939889	0.87[ASN][1000 genomes]
rs11943219	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12645501	1.00[JPT][hapmap]
rs13108474	0.85[EUR][1000 genomes]
rs13113370	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13119041	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs13119504	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13127730	0.82[EUR][1000 genomes]
rs13138269	0.82[EUR][1000 genomes]
rs13142540	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13149083	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.85[YRI][hapmap]
rs13151534	0.81[AMR][1000 genomes]
rs1507862	0.81[EUR][1000 genomes]
rs1507865	0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1517674	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1554256	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554258	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1589107	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1702798	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1712767	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17575720	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs17656040	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs17656094	1.00[JPT][hapmap]
rs1876469	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1980193	0.83[ASN][1000 genomes]
rs2056201	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2089503	0.82[EUR][1000 genomes]
rs2102397	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2176460	0.87[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2354312	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2354314	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2354348	0.82[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2572350	0.82[CHB][hapmap]
rs2712156	0.82[CHB][hapmap]
rs28470767	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs28733443	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34558821	0.83[EUR][1000 genomes]
rs3761729	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[MEX][hapmap];0.85[YRI][hapmap]
rs4536901	0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs4694906	0.83[CHB][hapmap]
rs4695391	0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4695397	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4695400	0.87[ASN][1000 genomes]
rs4695401	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4695407	0.95[CHB][hapmap];0.89[YRI][hapmap]
rs62309747	0.83[ASN][1000 genomes]
rs6447645	0.83[EUR][1000 genomes]
rs6447647	0.83[EUR][1000 genomes]
rs6447651	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447655	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447666	0.81[GIH][hapmap];0.85[YRI][hapmap]
rs6811148	1.00[JPT][hapmap]
rs6814811	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6818954	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819159	0.81[EUR][1000 genomes]
rs6830848	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6843340	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs6856448	0.83[EUR][1000 genomes]
rs7654032	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[YRI][hapmap]
rs7657332	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7657698	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7660206	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7661515	0.81[EUR][1000 genomes]
rs7667288	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7679210	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs7680280	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7681070	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7682859	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683398	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs7693461	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs7697522	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs776584	1.00[JPT][hapmap]
rs776588	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs776591	1.00[JPT][hapmap]
rs796555	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs9291326	0.95[CHB][hapmap];0.81[MEX][hapmap];0.89[YRI][hapmap]
rs937888	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs937889	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs952289	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs955683	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9790336	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9884546	0.81[EUR][1000 genomes]
rs9997920	0.95[CHB][hapmap];0.81[MEX][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv999203	chr4:48645887-48735512	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1802666	chr4:48646594-48721327	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013914	chr4:48652784-48728934	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv537090	chr4:48652784-48728934	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1796692	chr4:48686817-48726266	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7670939	OCIAD2	cis	lymphoblastoid	seeQTL
rs7670939	OCIAD2	cis	cerebellum	SCAN
rs7670939	SLC10A4	cis	lung	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48686800-48708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:48687000-48708400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:48687200-48708400	Weak transcription	Primary B cells from cord blood	blood
5	chr4:48690200-48705200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:48691600-48710400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:48695400-48711200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:48696600-48710600	Weak transcription	Lung	lung
9	chr4:48697200-48708600	Weak transcription	Left Ventricle	heart
10	chr4:48700000-48703600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:48700000-48703800	Enhancers	Fetal Intestine Small	intestine
12	chr4:48700000-48704000	Enhancers	Fetal Intestine Large	intestine
13	chr4:48700200-48730800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:48700400-48705200	Weak transcription	Dnd41	blood
15	chr4:48700400-48713200	Weak transcription	Placenta	Placenta
16	chr4:48700400-48718800	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:48700600-48704000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:48700600-48708000	Weak transcription	Fetal Thymus	thymus
19	chr4:48700600-48708400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:48700600-48719600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:48700800-48708000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:48700800-48708800	Weak transcription	Ovary	ovary
23	chr4:48700800-48712200	Weak transcription	Brain Germinal Matrix	brain
24	chr4:48700800-48715600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:48701000-48708600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:48701000-48710400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:48701000-48710600	Weak transcription	Adipose Nuclei	Adipose
28	chr4:48701000-48711200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:48701000-48712000	Weak transcription	Right Ventricle	heart
30	chr4:48701000-48712200	Weak transcription	Fetal Heart	heart
31	chr4:48701000-48713000	Weak transcription	Fetal Brain Male	brain
32	chr4:48701000-48715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:48701000-48729600	Weak transcription	Aorta	Aorta
34	chr4:48701200-48705200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:48701200-48708800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:48701200-48710600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:48701400-48705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr4:48701400-48713600	Weak transcription	Fetal Brain Female	brain
39	chr4:48701600-48705400	Weak transcription	Brain Anterior Caudate	brain
40	chr4:48701600-48706000	Weak transcription	Stomach Mucosa	stomach
41	chr4:48701800-48705000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:48701800-48705000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:48701800-48705000	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:48701800-48705200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:48701800-48705200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:48701800-48705400	Weak transcription	Psoas Muscle	Psoas
47	chr4:48701800-48710800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:48701800-48715400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:48701800-48715800	Weak transcription	Fetal Kidney	kidney
50	chr4:48701800-48724600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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