Variant report

Variant	rs10008265
Chromosome Location	chr4:48745442-48745443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10003273	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10010571	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10030853	0.82[AMR][1000 genomes]
rs10049761	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10938534	0.81[AMR][1000 genomes]
rs10938537	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs11727343	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11728565	0.85[AMR][1000 genomes]
rs11733534	0.82[CHB][hapmap];0.84[MEX][hapmap]
rs11737677	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes]
rs11939889	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11943219	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12503599	0.82[AMR][1000 genomes]
rs13108474	0.83[AMR][1000 genomes]
rs13108799	0.83[AMR][1000 genomes]
rs13113370	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119041	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs13119414	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13119504	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13138269	0.81[AMR][1000 genomes]
rs13142540	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13149083	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.81[YRI][hapmap]
rs13151534	0.84[AMR][1000 genomes]
rs1507862	0.81[AMR][1000 genomes]
rs1507865	0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1517674	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554256	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1554258	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1589107	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17575720	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs17656040	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs17656094	1.00[JPT][hapmap]
rs1876469	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs1980193	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2056201	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2085292	0.84[MEX][hapmap];0.85[YRI][hapmap]
rs2089503	0.81[AMR][1000 genomes]
rs2102397	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2176460	0.83[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290516	0.84[YRI][hapmap]
rs2354312	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2354314	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2354348	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs28470767	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs34558821	0.81[AMR][1000 genomes]
rs3761729	0.86[CHB][hapmap];0.84[MEX][hapmap];0.81[YRI][hapmap]
rs4536901	0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs4694904	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4695391	0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4695397	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4695400	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4695401	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4695407	0.91[CHB][hapmap];0.85[YRI][hapmap]
rs57797824	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6447645	0.81[AMR][1000 genomes]
rs6447647	0.81[AMR][1000 genomes]
rs6447651	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6447655	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6447666	0.81[GIH][hapmap];0.81[YRI][hapmap]
rs6814811	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6818954	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6819159	0.81[AMR][1000 genomes]
rs6830078	0.85[EUR][1000 genomes]
rs6830848	1.00[JPT][hapmap]
rs6843340	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs6856448	0.81[AMR][1000 genomes]
rs7654032	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[YRI][hapmap]
rs7657332	0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs7657698	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7660206	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7667288	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7670939	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7679210	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs7680280	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7681070	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7682859	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7683398	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs7693461	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs7697522	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs776584	1.00[JPT][hapmap]
rs776591	1.00[JPT][hapmap]
rs796555	0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs9291326	0.91[CHB][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap]
rs937889	1.00[JPT][hapmap]
rs952289	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs955683	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9790336	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9997920	0.91[CHB][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
8	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
9	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
10	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
11	esv1792281	chr4:48719424-48764009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1794245	chr4:48719424-48764009	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1794757	chr4:48719424-48764009	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10008265	OCIAD2	cis	cerebellum	SCAN
rs10008265	SLC10A4	cis	lung	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48751000	Weak transcription	Lung	lung
2	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:48738000-48746800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr4:48738200-48746600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr4:48738200-48747000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:48739400-48745600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr4:48739400-48747200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr4:48740400-48746400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:48740800-48746000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr4:48741000-48751200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:48741400-48745600	Enhancers	Primary T cells from cord blood	blood
12	chr4:48741400-48747000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:48742000-48758800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:48742000-48768400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:48742600-48745800	Enhancers	Dnd41	blood
16	chr4:48742600-48751200	Weak transcription	Esophagus	oesophagus
17	chr4:48742600-48768200	Weak transcription	Pancreas	Pancrea
18	chr4:48742800-48753800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:48743000-48748600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:48743000-48748600	Weak transcription	Liver	Liver
21	chr4:48743200-48748600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:48743200-48748600	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:48743200-48748800	Weak transcription	Brain Anterior Caudate	brain
24	chr4:48743600-48748200	Weak transcription	Right Atrium	heart
25	chr4:48743800-48745800	Enhancers	GM12878-XiMat	blood
26	chr4:48744200-48748200	Weak transcription	Left Ventricle	heart
27	chr4:48744200-48749000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:48744400-48749000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:48744400-48750400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:48744600-48748600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:48744600-48748600	Weak transcription	Gastric	stomach
32	chr4:48744600-48748600	Weak transcription	Thymus	Thymus
33	chr4:48744600-48748600	Weak transcription	HMEC	breast
34	chr4:48744600-48748600	Weak transcription	K562	blood
35	chr4:48744600-48748800	Weak transcription	Brain Angular Gyrus	brain
36	chr4:48744600-48750400	Weak transcription	Right Ventricle	heart
37	chr4:48744600-48751200	Weak transcription	Brain Substantia Nigra	brain
38	chr4:48744600-48752800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:48744600-48753000	Weak transcription	Osteobl	bone
40	chr4:48744800-48746600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:48744800-48748000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:48744800-48748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:48744800-48748800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:48744800-48749000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:48744800-48750800	Weak transcription	Fetal Heart	heart
46	chr4:48744800-48753600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:48745000-48748000	Weak transcription	NHEK	skin
48	chr4:48745000-48748600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:48745000-48750000	Weak transcription	Psoas Muscle	Psoas
50	chr4:48745000-48750600	Weak transcription	Primary hematopoietic stem cells	blood

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