Variant report

Variant	rs778517
Chromosome Location	chr3:23528977-23528978
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10510539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11129120	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706875	0.95[ASN][1000 genomes]
rs11712991	1.00[ASN][1000 genomes]
rs11713090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715736	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11717508	0.97[ASN][1000 genomes]
rs11718111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13316118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13323077	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1391756	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498810	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1498812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1692619	0.94[CEU][hapmap]
rs1692621	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1692646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692647	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1692648	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695180	0.94[CEU][hapmap]
rs1695183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695192	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1695197	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695203	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs17013268	0.94[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.93[ASN][1000 genomes]
rs17013425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17194751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1874234	0.94[CEU][hapmap];0.84[JPT][hapmap]
rs1874502	0.94[CEU][hapmap]
rs1874503	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs1995173	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995174	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995175	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2036044	0.94[CEU][hapmap]
rs2055307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173057	0.94[CEU][hapmap]
rs2359761	0.94[CEU][hapmap]
rs28367247	1.00[ASN][1000 genomes]
rs4858070	0.94[CEU][hapmap]
rs4858495	0.94[CEU][hapmap]
rs4858499	0.88[CEU][hapmap]
rs4858507	0.94[CEU][hapmap]
rs4858517	0.95[ASN][1000 genomes]
rs56034809	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58130044	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58618629	0.95[ASN][1000 genomes]
rs58718028	0.86[EUR][1000 genomes]
rs59012069	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60028742	0.98[ASN][1000 genomes]
rs60137984	1.00[ASN][1000 genomes]
rs62255784	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255785	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255789	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62256025	0.99[ASN][1000 genomes]
rs62256972	0.99[ASN][1000 genomes]
rs62256973	1.00[ASN][1000 genomes]
rs62256975	1.00[ASN][1000 genomes]
rs62256976	1.00[ASN][1000 genomes]
rs62256977	1.00[ASN][1000 genomes]
rs62256982	1.00[ASN][1000 genomes]
rs62256990	0.97[ASN][1000 genomes]
rs62256991	0.95[ASN][1000 genomes]
rs6550760	0.93[CEU][hapmap]
rs66864142	0.93[ASN][1000 genomes]
rs6774454	1.00[ASN][1000 genomes]
rs6780388	0.94[CEU][hapmap]
rs6801824	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs6807859	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68093882	1.00[ASN][1000 genomes]
rs73139773	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140507	0.94[ASN][1000 genomes]
rs73140523	0.98[ASN][1000 genomes]
rs73140544	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430428	1.00[ASN][1000 genomes]
rs7614195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643705	0.94[CEU][hapmap]
rs7646541	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778463	0.94[CEU][hapmap]
rs778465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778473	0.91[ASN][1000 genomes]
rs778483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778491	0.82[EUR][1000 genomes]
rs778492	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs778497	0.94[CEU][hapmap];0.93[CHB][hapmap];0.92[ASN][1000 genomes]
rs778502	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs778511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778512	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778515	0.84[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs778516	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778520	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778524	0.85[CEU][hapmap]
rs778525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801277	0.85[CEU][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs809640	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931609	0.94[CEU][hapmap]
rs9631541	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs9757330	0.94[CEU][hapmap]
rs9758590	0.94[CEU][hapmap]
rs9815299	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs9862734	0.84[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv3434857	chr3:23527314-23531055	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23521000-23531800	Weak transcription	NHDF-Ad	bronchial
2	chr3:23521600-23532000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:23522000-23531000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:23522000-23531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:23523000-23530800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:23523200-23536800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:23523400-23531000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:23523600-23542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:23524000-23534800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:23524800-23531000	Weak transcription	Psoas Muscle	Psoas
11	chr3:23526000-23532000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:23526600-23554000	Weak transcription	Primary T cells from cord blood	blood
13	chr3:23527400-23529000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:23527400-23529000	ZNF genes & repeats	Fetal Stomach	stomach
15	chr3:23527600-23529400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:23527800-23533200	Weak transcription	Aorta	Aorta
17	chr3:23528000-23531000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:23528000-23542200	Weak transcription	Right Ventricle	heart
19	chr3:23528200-23531000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:23528400-23529400	Weak transcription	Fetal Heart	heart
21	chr3:23528400-23530400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:23528400-23531400	Weak transcription	NHLF	lung
23	chr3:23528600-23529000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:23528600-23529200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:23528600-23530800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:23528600-23531400	Weak transcription	Brain Anterior Caudate	brain
27	chr3:23528600-23542200	Weak transcription	Primary B cells from cord blood	blood
28	chr3:23528600-23552200	Weak transcription	Ovary	ovary
29	chr3:23528800-23529000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:23528800-23529200	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:23528800-23530800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:23528800-23530800	Weak transcription	Right Atrium	heart
33	chr3:23528800-23531000	Weak transcription	Left Ventricle	heart
34	chr3:23528800-23531000	Weak transcription	Spleen	Spleen
35	chr3:23528800-23531200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:23528800-23536600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:23528800-23536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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