Variant report

Variant	rs1692649
Chromosome Location	chr3:23522285-23522286
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10510539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11129120	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706875	0.92[ASN][1000 genomes]
rs11712991	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11713090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715736	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717508	0.94[ASN][1000 genomes]
rs11718111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13316118	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]
rs13323077	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs1391756	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498810	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1498812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1692619	0.94[CEU][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs1692621	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1692646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1692647	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs1692648	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1695185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1695192	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1695197	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1695203	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs17013268	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs17013425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17194751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[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	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1995174	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1995175	0.85[CEU][hapmap];0.87[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];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.99[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];0.92[JPT][hapmap]
rs4858495	0.94[CEU][hapmap];0.86[JPT][hapmap]
rs4858499	0.88[CEU][hapmap]
rs4858507	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs4858517	0.92[ASN][1000 genomes]
rs56034809	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58130044	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58618629	0.92[ASN][1000 genomes]
rs58718028	0.84[EUR][1000 genomes]
rs59012069	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60028742	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs60137984	0.97[ASN][1000 genomes]
rs62255784	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62255785	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62255789	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62256025	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62256972	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62256973	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62256975	0.97[ASN][1000 genomes]
rs62256976	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62256977	0.85[AFR][1000 genomes];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	0.85[AFR][1000 genomes];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	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68093882	0.97[ASN][1000 genomes]
rs73139773	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73140507	0.97[ASN][1000 genomes]
rs73140523	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73140544	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7430428	0.97[ASN][1000 genomes]
rs7614195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7643705	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs7646541	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778463	0.94[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs778465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778473	0.93[ASN][1000 genomes]
rs778479	0.80[EUR][1000 genomes]
rs778483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778491	0.84[EUR][1000 genomes]
rs778492	0.94[CEU][hapmap];0.92[CHB][hapmap];0.91[ASN][1000 genomes]
rs778497	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs778502	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs778511	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778512	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778515	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778516	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778520	0.85[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs778522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[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];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs801277	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs809640	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs875443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs931609	0.94[CEU][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs9631541	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs9757330	0.94[CEU][hapmap];0.93[JPT][hapmap]
rs9758590	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs9815299	0.94[CEU][hapmap];0.90[YRI][hapmap]
rs9862734	0.85[CEU][hapmap];0.87[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:51 , 50 per page) page: 1 2

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	chr3:23521000-23522800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:23521000-23527600	Weak transcription	Right Ventricle	heart
7	chr3:23521000-23531800	Weak transcription	NHDF-Ad	bronchial
8	chr3:23521200-23523000	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:23521200-23527600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:23521400-23522600	Weak transcription	Fetal Kidney	kidney
11	chr3:23521400-23522600	Weak transcription	Fetal Lung	lung
12	chr3:23521400-23523400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:23521600-23522600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:23521600-23522600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr3:23521600-23523400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:23521600-23527400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:23521600-23532000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:23521800-23522400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:23521800-23523000	Weak transcription	Brain Angular Gyrus	brain
20	chr3:23521800-23523000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:23521800-23523600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:23521800-23524000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr3:23521800-23527400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:23521800-23527600	Weak transcription	Spleen	Spleen
25	chr3:23521800-23528600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:23522000-23522400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:23522000-23522600	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:23522000-23523000	Weak transcription	HSMMtube	muscle
29	chr3:23522000-23523200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:23522000-23525800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:23522000-23527400	Weak transcription	Thymus	Thymus
32	chr3:23522000-23527400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:23522000-23527800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:23522000-23531000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:23522000-23531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:23522200-23522400	Weak transcription	Lung	lung
37	chr3:23522200-23522600	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr3:23522200-23522600	Active TSS	Brain Substantia Nigra	brain
39	chr3:23522200-23522600	Weak transcription	GM12878-XiMat	blood
40	chr3:23522200-23522800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr3:23522200-23522800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:23522200-23523000	Active TSS	Brain Anterior Caudate	brain
43	chr3:23522200-23523200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:23522200-23523200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:23522200-23523200	Enhancers	Brain Germinal Matrix	brain
46	chr3:23522200-23523800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr3:23522200-23527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:23522200-23527400	Weak transcription	Primary B cells from cord blood	blood
49	chr3:23522200-23527600	Weak transcription	Fetal Thymus	thymus
50	chr3:23522200-23527800	Weak transcription	Fetal Muscle Trunk	muscle

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