Variant report

Variant	rs1692647
Chromosome Location	chr3:23522809-23522810
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10510539	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs11129120	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs11713090	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11715736	0.84[EUR][1000 genomes]
rs11718111	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs13316118	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs13323077	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]
rs1391756	0.84[EUR][1000 genomes]
rs1498810	0.87[EUR][1000 genomes]
rs1498812	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs1692621	0.85[CEU][hapmap]
rs1692646	0.85[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1692648	0.87[EUR][1000 genomes]
rs1692649	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs1695180	0.81[CEU][hapmap]
rs1695183	0.85[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1695185	0.84[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1695192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1695197	0.86[EUR][1000 genomes]
rs1695203	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17013268	0.81[CEU][hapmap]
rs17013425	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17194751	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs1874502	0.80[CEU][hapmap]
rs1874503	0.81[CEU][hapmap]
rs1995173	0.84[EUR][1000 genomes]
rs1995174	0.86[EUR][1000 genomes]
rs1995175	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036044	0.81[CEU][hapmap]
rs2047340	0.90[JPT][hapmap]
rs2055155	0.95[CEU][hapmap];0.80[JPT][hapmap]
rs2055307	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs56034809	0.88[EUR][1000 genomes]
rs58130044	0.84[EUR][1000 genomes]
rs58718028	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59012069	0.86[EUR][1000 genomes]
rs62255784	0.87[EUR][1000 genomes]
rs62255785	0.86[EUR][1000 genomes]
rs62255789	0.84[EUR][1000 genomes]
rs62256989	0.91[ASN][1000 genomes]
rs6550754	0.90[CEU][hapmap]
rs6780388	0.81[CEU][hapmap]
rs6790185	0.80[JPT][hapmap]
rs6790327	0.81[CEU][hapmap]
rs6801824	0.81[CEU][hapmap]
rs6807859	0.85[EUR][1000 genomes]
rs73139773	0.86[EUR][1000 genomes]
rs73140544	0.88[EUR][1000 genomes]
rs7431560	0.86[ASN][1000 genomes]
rs7614195	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs7629327	0.95[CEU][hapmap];0.84[JPT][hapmap]
rs7636705	0.85[CEU][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7643705	0.81[CEU][hapmap]
rs7646541	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648425	0.95[CEU][hapmap]
rs778465	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs778479	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778483	0.85[CEU][hapmap]
rs778489	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs778491	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs778492	0.80[CEU][hapmap]
rs778502	0.85[CEU][hapmap]
rs778511	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs778512	0.86[EUR][1000 genomes]
rs778513	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs778515	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs778516	0.86[EUR][1000 genomes]
rs778517	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778518	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs778519	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs778520	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs778522	0.85[CEU][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs778524	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs778525	0.85[CEU][hapmap]
rs778527	0.85[CEU][hapmap]
rs801277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs809640	0.86[EUR][1000 genomes]
rs875443	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9631541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9757330	0.81[CEU][hapmap]
rs9758590	0.81[CEU][hapmap]
rs9862734	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][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:58 , 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	chr3:23513800-23527400	Weak transcription	Right Atrium	heart
4	chr3:23521000-23527600	Weak transcription	Right Ventricle	heart
5	chr3:23521000-23531800	Weak transcription	NHDF-Ad	bronchial
6	chr3:23521200-23523000	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:23521200-23527600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:23521400-23523400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:23521600-23523400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:23521600-23527400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:23521600-23532000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:23521800-23523000	Weak transcription	Brain Angular Gyrus	brain
13	chr3:23521800-23523000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:23521800-23523600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:23521800-23524000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:23521800-23527400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:23521800-23527600	Weak transcription	Spleen	Spleen
18	chr3:23521800-23528600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:23522000-23523000	Weak transcription	HSMMtube	muscle
20	chr3:23522000-23523200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:23522000-23525800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr3:23522000-23527400	Weak transcription	Thymus	Thymus
23	chr3:23522000-23527400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr3:23522000-23527800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:23522000-23531000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:23522000-23531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:23522200-23523000	Active TSS	Brain Anterior Caudate	brain
28	chr3:23522200-23523200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:23522200-23523200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:23522200-23523200	Enhancers	Brain Germinal Matrix	brain
31	chr3:23522200-23523800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:23522200-23527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:23522200-23527400	Weak transcription	Primary B cells from cord blood	blood
34	chr3:23522200-23527600	Weak transcription	Fetal Thymus	thymus
35	chr3:23522200-23527800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:23522200-23528000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:23522400-23523600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:23522400-23524000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr3:23522600-23523200	Enhancers	Fetal Brain Female	brain
40	chr3:23522600-23523400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:23522600-23523400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr3:23522600-23523600	Enhancers	Brain Substantia Nigra	brain
43	chr3:23522600-23523600	Enhancers	Fetal Brain Male	brain
44	chr3:23522600-23523600	Enhancers	Fetal Kidney	kidney
45	chr3:23522600-23523600	Enhancers	GM12878-XiMat	blood
46	chr3:23522600-23523800	Enhancers	Fetal Lung	lung
47	chr3:23522600-23524000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr3:23522600-23524000	Enhancers	Brain Hippocampus Middle	brain
49	chr3:23522600-23524000	Enhancers	Fetal Muscle Leg	muscle
50	chr3:23522800-23523000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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