Variant report

Variant	rs10875098
Chromosome Location	chr1:98041720-98041721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10783069	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783070	0.83[ASW][hapmap];0.88[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875099	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165895	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073839	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs12122032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1337522	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1337523	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065943	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248658	0.80[TSI][hapmap]
rs2485436	0.87[ASN][1000 genomes]
rs2786494	0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs2786496	0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs2786498	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2786500	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs2786501	0.87[CEU][hapmap]
rs2786503	0.86[GIH][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2786504	0.91[EUR][1000 genomes]
rs2786505	0.87[CEU][hapmap]
rs2786541	0.87[ASN][1000 genomes]
rs2786543	0.80[TSI][hapmap]
rs2786544	0.88[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2811192	0.83[CHD][hapmap]
rs2811193	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2811194	0.88[EUR][1000 genomes]
rs2811195	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2811196	0.86[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2811197	0.91[EUR][1000 genomes]
rs2811199	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2811200	0.87[CEU][hapmap]
rs2811201	0.90[EUR][1000 genomes]
rs2811203	0.86[GIH][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2811205	0.87[ASN][1000 genomes]
rs2811206	0.87[ASN][1000 genomes]
rs2811208	0.87[ASN][1000 genomes]
rs2811210	0.93[EUR][1000 genomes]
rs2811211	0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs2811212	0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs2811214	0.87[CEU][hapmap];0.80[TSI][hapmap]
rs2811215	0.85[GIH][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs4949958	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663357	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663670	0.88[CEU][hapmap]
rs6691128	0.87[ASN][1000 genomes]
rs7512910	0.88[CEU][hapmap]
rs7533902	0.83[ASW][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7537165	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv830703	chr1:97907708-98101144	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv871708	chr1:98003908-98056575	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv546866	chr1:98003908-98078993	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv830714	chr1:98025090-98229416	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	esv3452393	chr1:98037725-98042813	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3452394	chr1:98037725-98042813	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3452392	chr1:98037752-98042810	Strong transcription Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3692791	chr1:98038091-98041720	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv528034	chr1:98038179-98041720	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv518604	chr1:98038179-98050656	Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv521057	chr1:98041720-98050656	Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97976600-98054200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:97976800-98051400	Weak transcription	Left Ventricle	heart
3	chr1:97998600-98063800	Weak transcription	Right Ventricle	heart
4	chr1:97999400-98064600	Weak transcription	Psoas Muscle	Psoas
5	chr1:97999400-98074000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:98001200-98062400	Weak transcription	Fetal Lung	lung
7	chr1:98002000-98054600	Weak transcription	Lung	lung
8	chr1:98002000-98069400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:98002800-98058800	Weak transcription	Gastric	stomach
10	chr1:98004400-98058400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:98007800-98058400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:98007800-98075800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:98009800-98076800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:98009800-98112200	Weak transcription	HSMM	muscle
15	chr1:98012000-98054200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:98013400-98048600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:98013600-98058800	Weak transcription	Esophagus	oesophagus
18	chr1:98015200-98047000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:98015200-98054000	Weak transcription	Adipose Nuclei	Adipose
20	chr1:98015200-98058600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:98015200-98062000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:98015600-98058600	Weak transcription	Osteobl	bone
23	chr1:98020000-98059000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:98020000-98060600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:98023200-98045400	Weak transcription	Fetal Intestine Small	intestine
26	chr1:98023800-98053000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:98025200-98046600	Weak transcription	Thymus	Thymus
28	chr1:98026000-98051400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:98026600-98051200	Weak transcription	Primary B cells from cord blood	blood
30	chr1:98028800-98054200	Weak transcription	Ovary	ovary
31	chr1:98034200-98047000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:98036800-98064400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:98037200-98060600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:98037600-98050600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:98037600-98059800	Weak transcription	Fetal Thymus	thymus
36	chr1:98038600-98056200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:98039600-98042200	Weak transcription	Liver	Liver
38	chr1:98039600-98053800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:98039600-98053800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:98039600-98054200	Weak transcription	Dnd41	blood
41	chr1:98039600-98058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:98039600-98060400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:98039800-98052000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:98039800-98052200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:98039800-98054200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:98039800-98054200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:98039800-98055400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:98040400-98042800	Weak transcription	Primary T cells from cord blood	blood
49	chr1:98041000-98043800	Weak transcription	Primary monocytes fromperipheralblood	blood

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