Variant report

Variant	rs6447651
Chromosome Location	chr4:48709424-48709425
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	chr4:48702489..48705093-chr4:48707646..48709743,2	MCF-7	breast:

Extended variants
information (count: 117 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10003273	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10008265	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10010571	0.82[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];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938534	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs10938537	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11727343	0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap]
rs11728565	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11733534	0.91[CHB][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs11734019	0.81[EUR][1000 genomes]
rs11737677	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.82[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]
rs12512637	0.81[CHB][hapmap]
rs13108474	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13108799	0.80[AMR][1000 genomes]
rs13113370	0.81[AFR][1000 genomes];1.00[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];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap]
rs13119504	0.90[AFR][1000 genomes];0.91[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	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13149083	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[MEX][hapmap];0.81[YRI][hapmap]
rs13151534	0.82[AMR][1000 genomes]
rs1507862	0.81[EUR][1000 genomes]
rs1507865	0.95[GIH][hapmap];0.95[JPT][hapmap]
rs1517674	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1554256	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554258	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1589107	0.95[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];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs17656040	0.84[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs17656094	0.95[JPT][hapmap]
rs1876469	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1980193	0.83[ASN][1000 genomes]
rs2056201	0.87[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];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2176460	0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs2290516	0.81[CHB][hapmap];0.83[YRI][hapmap]
rs2354312	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2354314	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2354348	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2572345	0.81[CHB][hapmap]
rs2572350	0.86[CHB][hapmap]
rs2712156	0.86[CHB][hapmap]
rs28470767	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];1.00[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	0.95[CHB][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap]
rs4536901	0.93[GIH][hapmap];0.95[JPT][hapmap]
rs4694906	0.86[CHB][hapmap]
rs4695391	0.91[GIH][hapmap];0.95[JPT][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	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs62309747	0.83[ASN][1000 genomes]
rs6447645	0.83[EUR][1000 genomes]
rs6447647	0.83[EUR][1000 genomes]
rs6447655	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447666	0.83[GIH][hapmap];0.81[YRI][hapmap]
rs6811148	0.95[JPT][hapmap]
rs6814811	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6818954	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819159	0.81[EUR][1000 genomes]
rs6830848	0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6843340	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6856448	0.83[EUR][1000 genomes]
rs7654032	0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[YRI][hapmap]
rs7657332	0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs7657698	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7660206	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7661515	0.81[EUR][1000 genomes]
rs7665209	0.81[CHB][hapmap]
rs7667288	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7670939	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679210	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[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	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683398	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs7693461	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs7697522	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs776584	0.95[JPT][hapmap]
rs776588	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs776591	0.95[JPT][hapmap]
rs796555	0.93[GIH][hapmap];0.95[JPT][hapmap]
rs9291326	1.00[CHB][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap]
rs937888	0.93[GIH][hapmap];0.95[JPT][hapmap]
rs937889	0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs952289	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs955683	0.85[AFR][1000 genomes];0.89[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	1.00[CHB][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.85[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
rs6447651	OCIAD2	cis	cerebellum	SCAN
rs6447651	SLC10A4	cis	lung	GTEx
rs6447651	OCIAD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48691600-48710400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:48695400-48711200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:48696600-48710600	Weak transcription	Lung	lung
5	chr4:48700200-48730800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:48700400-48713200	Weak transcription	Placenta	Placenta
7	chr4:48700400-48718800	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:48700600-48719600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:48700800-48712200	Weak transcription	Brain Germinal Matrix	brain
10	chr4:48700800-48715600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:48701000-48710400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:48701000-48710600	Weak transcription	Adipose Nuclei	Adipose
13	chr4:48701000-48711200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:48701000-48712000	Weak transcription	Right Ventricle	heart
15	chr4:48701000-48712200	Weak transcription	Fetal Heart	heart
16	chr4:48701000-48713000	Weak transcription	Fetal Brain Male	brain
17	chr4:48701000-48715200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:48701000-48729600	Weak transcription	Aorta	Aorta
19	chr4:48701200-48710600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr4:48701400-48713600	Weak transcription	Fetal Brain Female	brain
21	chr4:48701800-48710800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:48701800-48715400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:48701800-48715800	Weak transcription	Fetal Kidney	kidney
24	chr4:48701800-48724600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:48702000-48710400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:48702200-48716200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:48702400-48710600	Weak transcription	Liver	Liver
28	chr4:48702400-48711200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:48702600-48710400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:48702600-48710600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:48702600-48710800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:48702600-48711200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:48702600-48717400	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:48702800-48710800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr4:48702800-48711200	Weak transcription	GM12878-XiMat	blood
36	chr4:48702800-48712400	Weak transcription	HUVEC	blood vessel
37	chr4:48702800-48720800	Weak transcription	Small Intestine	intestine
38	chr4:48703000-48711200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:48703200-48711400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:48703400-48714800	Weak transcription	NH-A	brain
41	chr4:48703400-48722800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr4:48703600-48711200	Weak transcription	NHDF-Ad	bronchial
43	chr4:48703800-48712600	Weak transcription	Osteobl	bone
44	chr4:48704000-48710600	Weak transcription	Fetal Intestine Large	intestine
45	chr4:48704000-48711400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:48704000-48711800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:48704000-48712200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:48704000-48712600	Weak transcription	Fetal Stomach	stomach
49	chr4:48705600-48710600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:48705600-48712800	Weak transcription	Psoas Muscle	Psoas

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