Variant report

Variant	rs13316118
Chromosome Location	chr3:23520877-23520878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10510539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11129120	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706875	0.92[ASN][1000 genomes]
rs11712991	0.97[ASN][1000 genomes]
rs11713090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715736	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717508	0.94[ASN][1000 genomes]
rs11718111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13323077	0.85[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1391756	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498810	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1498812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1692619	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs1692621	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1692646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1692647	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1692648	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1692649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1695180	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs1695183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1695185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1695192	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1695197	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1695203	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs17013268	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17013425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17194751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1874234	0.94[CEU][hapmap]
rs1874502	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs1874503	0.94[CEU][hapmap]
rs1995173	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1995174	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1995175	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2036044	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs2036045	1.00[JPT][hapmap]
rs2055307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2173057	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs2359761	0.94[CEU][hapmap];0.86[JPT][hapmap]
rs28367247	0.97[ASN][1000 genomes]
rs4858070	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs4858495	0.94[CEU][hapmap];0.87[JPT][hapmap]
rs4858499	0.88[CEU][hapmap]
rs4858507	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs4858517	0.92[ASN][1000 genomes]
rs56034809	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58130044	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58618629	0.92[ASN][1000 genomes]
rs58718028	0.83[EUR][1000 genomes]
rs59012069	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60028742	0.95[ASN][1000 genomes]
rs60137984	0.97[ASN][1000 genomes]
rs62255784	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62255785	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62255789	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62256025	0.96[ASN][1000 genomes]
rs62256972	0.96[ASN][1000 genomes]
rs62256973	0.97[ASN][1000 genomes]
rs62256975	0.97[ASN][1000 genomes]
rs62256976	0.97[ASN][1000 genomes]
rs62256977	0.97[ASN][1000 genomes]
rs62256982	0.97[ASN][1000 genomes]
rs62256990	0.94[ASN][1000 genomes]
rs62256991	0.92[ASN][1000 genomes]
rs6550760	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs66864142	0.90[ASN][1000 genomes]
rs6774454	0.97[ASN][1000 genomes]
rs6780388	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs6790327	0.94[CEU][hapmap]
rs6801824	0.94[CEU][hapmap]
rs6807859	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68093882	0.97[ASN][1000 genomes]
rs73139773	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73140507	0.97[ASN][1000 genomes]
rs73140523	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73140544	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7430428	0.97[ASN][1000 genomes]
rs7614195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7643705	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs7646541	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs778463	0.94[CEU][hapmap];0.86[JPT][hapmap]
rs778465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778473	0.93[ASN][1000 genomes]
rs778479	0.82[EUR][1000 genomes]
rs778483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778491	0.85[EUR][1000 genomes]
rs778492	0.94[CEU][hapmap];0.92[CHB][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778497	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778502	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778512	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778515	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs778516	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778517	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]
rs778518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778520	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs778522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778524	0.85[CEU][hapmap]
rs778525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs801277	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs809640	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs875443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs931609	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs9631541	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9757330	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs9758590	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs9815299	0.94[CEU][hapmap]
rs9848389	0.94[CEU][hapmap]
rs9862734	0.85[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23512000-23523000	Weak transcription	Psoas Muscle	Psoas
2	chr3:23512000-23527400	Weak transcription	Left Ventricle	heart
3	chr3:23513400-23522800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:23513800-23527400	Weak transcription	Right Atrium	heart
5	chr3:23516800-23521200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:23517000-23521200	Weak transcription	HSMMtube	muscle
7	chr3:23517000-23522000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:23517400-23521800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:23518800-23522000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr3:23519400-23522200	ZNF genes & repeats	Primary B cells from cord blood	blood
11	chr3:23520400-23521800	ZNF genes & repeats	Thymus	Thymus
12	chr3:23520400-23522200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr3:23520400-23522200	ZNF genes & repeats	Fetal Thymus	thymus
14	chr3:23520600-23521000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:23520600-23521000	Enhancers	Right Ventricle	heart
16	chr3:23520600-23521000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:23520600-23521000	Enhancers	NHDF-Ad	bronchial
18	chr3:23520600-23521200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:23520600-23521400	Enhancers	Esophagus	oesophagus
20	chr3:23520600-23521600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr3:23520600-23521800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:23520600-23521800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:23520600-23521800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:23520600-23521800	ZNF genes & repeats	Spleen	Spleen
25	chr3:23520600-23522000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:23520600-23522000	ZNF genes & repeats	Lung	lung
27	chr3:23520600-23522200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:23520600-23522200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:23520600-23522200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr3:23520600-23522200	ZNF genes & repeats	GM12878-XiMat	blood
31	chr3:23520800-23521000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:23520800-23521000	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr3:23520800-23521000	Enhancers	Brain Angular Gyrus	brain
34	chr3:23520800-23521200	Enhancers	HMEC	breast
35	chr3:23520800-23521400	ZNF genes & repeats	Fetal Lung	lung
36	chr3:23520800-23522000	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr3:23520800-23522000	ZNF genes & repeats	Pancreas	Pancrea

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