Variant report

Variant	rs1337523
Chromosome Location	chr1:98061402-98061403
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	chr1:98055044..98057543-chr1:98059775..98062568,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10783069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783070	0.94[ASW][hapmap];0.89[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875098	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]
rs10875099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875100	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165895	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073839	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs12122032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1337522	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13375275	0.81[EUR][1000 genomes]
rs13375516	0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs2065943	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	0.89[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2786500	0.89[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap]
rs2786503	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs2786504	0.94[EUR][1000 genomes]
rs2786541	0.87[ASN][1000 genomes]
rs2786544	0.89[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2811192	0.83[CHD][hapmap]
rs2811193	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2811194	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2811195	0.89[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs2811196	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2811197	0.94[EUR][1000 genomes]
rs2811199	0.89[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs2811201	0.93[EUR][1000 genomes]
rs2811203	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs2811205	0.87[ASN][1000 genomes]
rs2811206	0.87[ASN][1000 genomes]
rs2811208	0.87[ASN][1000 genomes]
rs2811210	0.92[EUR][1000 genomes]
rs2811211	0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs2811212	0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs2811215	0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs4949958	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663357	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663670	0.89[CEU][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs6691128	0.87[ASN][1000 genomes]
rs67086927	0.81[EUR][1000 genomes]
rs72975761	0.81[EUR][1000 genomes]
rs72975765	0.81[EUR][1000 genomes]
rs72975785	0.81[EUR][1000 genomes]
rs72975790	0.81[EUR][1000 genomes]
rs7512910	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7533902	0.94[ASW][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs7537165	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
6	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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97998600-98063800	Weak transcription	Right Ventricle	heart
2	chr1:97999400-98064600	Weak transcription	Psoas Muscle	Psoas
3	chr1:97999400-98074000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:98001200-98062400	Weak transcription	Fetal Lung	lung
5	chr1:98002000-98069400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:98007800-98075800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:98009800-98076800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:98009800-98112200	Weak transcription	HSMM	muscle
9	chr1:98015200-98062000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:98036800-98064400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:98041800-98074000	Weak transcription	Aorta	Aorta
12	chr1:98047600-98069000	Weak transcription	NHDF-Ad	bronchial
13	chr1:98048000-98069400	Weak transcription	NHLF	lung
14	chr1:98051600-98076600	Weak transcription	Spleen	Spleen
15	chr1:98051800-98096000	Weak transcription	Left Ventricle	heart
16	chr1:98053000-98061800	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:98054000-98069000	Weak transcription	Brain Substantia Nigra	brain
18	chr1:98055200-98065200	Weak transcription	Lung	lung
19	chr1:98056800-98062200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:98056800-98063000	Weak transcription	Primary T cells from cord blood	blood
21	chr1:98057000-98065000	Weak transcription	HMEC	breast
22	chr1:98058600-98063000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:98059000-98062000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:98059000-98062800	Weak transcription	Gastric	stomach
25	chr1:98059000-98069600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:98059200-98063800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:98059200-98064400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:98059200-98069800	Weak transcription	Adipose Nuclei	Adipose
29	chr1:98059200-98070400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:98059400-98061600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:98059600-98076800	Weak transcription	Primary B cells from cord blood	blood
32	chr1:98060000-98066400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:98060000-98087400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:98060200-98065200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:98060400-98062000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:98060600-98062600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:98060600-98069200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:98060800-98062200	Weak transcription	Liver	Liver
39	chr1:98060800-98062400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:98060800-98062600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:98060800-98062600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:98060800-98062600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:98060800-98063000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:98060800-98063800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:98060800-98092400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:98061000-98062800	Weak transcription	Dnd41	blood
47	chr1:98061200-98062000	Weak transcription	Monocytes-CD14+_RO01746	blood

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