Variant report

Variant	rs11129120
Chromosome Location	chr3:23578763-23578764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10510539	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706875	0.95[ASN][1000 genomes]
rs11712991	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11713090	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715736	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11717508	0.97[ASN][1000 genomes]
rs11718111	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13316118	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13323077	0.85[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1391756	1.00[ASW][hapmap];0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498810	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1498812	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1692619	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[GIH][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs1692621	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1692646	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692647	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1692648	0.92[CHB][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692649	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]
rs1695180	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs1695183	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695185	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695192	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1695197	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695203	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17013268	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs17013425	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17194751	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1874234	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs1874502	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs1874503	0.94[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs1995173	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995174	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995175	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2036044	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs2036045	0.91[YRI][hapmap]
rs2055307	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173057	0.94[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap]
rs2359761	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs28367247	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4858070	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs4858507	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs4858517	0.95[ASN][1000 genomes]
rs56034809	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58130044	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58618629	0.95[ASN][1000 genomes]
rs58718028	0.84[EUR][1000 genomes]
rs59012069	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60028742	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs60137984	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62255784	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255785	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255789	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62256025	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62256972	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62256973	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62256975	1.00[ASN][1000 genomes]
rs62256976	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62256977	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62256982	1.00[ASN][1000 genomes]
rs62256990	0.97[ASN][1000 genomes]
rs62256991	0.95[ASN][1000 genomes]
rs6550760	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs66864142	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6774454	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6780388	0.94[CEU][hapmap]
rs6801824	0.94[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs6807859	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68093882	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73139773	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140507	0.94[ASN][1000 genomes]
rs73140523	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs73140544	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430428	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7614195	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636705	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643705	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs7646541	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs778463	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[GIH][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs778465	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778473	0.91[ASN][1000 genomes]
rs778483	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778489	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778492	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs778497	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs778502	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs778511	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778512	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778513	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778515	0.85[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs778516	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778517	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778518	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778519	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778520	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs778522	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778524	0.85[CEU][hapmap]
rs778525	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778527	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801277	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs809640	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875443	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931609	0.94[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs9631541	0.85[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs9757330	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs9758590	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs9862734	0.85[CEU][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.82[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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23550800-23598600	Weak transcription	HSMMtube	muscle
2	chr3:23553000-23589600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:23567400-23589800	Weak transcription	Psoas Muscle	Psoas
4	chr3:23570600-23584400	Weak transcription	Primary T cells from cord blood	blood
5	chr3:23571200-23591600	Weak transcription	GM12878-XiMat	blood
6	chr3:23571400-23598800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:23572800-23579400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:23573800-23578800	Strong transcription	Primary B cells from cord blood	blood
9	chr3:23574800-23579800	Weak transcription	Aorta	Aorta
10	chr3:23575600-23578800	Weak transcription	Fetal Lung	lung
11	chr3:23578000-23579400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:23578000-23579600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:23578000-23579800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:23578200-23579000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:23578200-23579200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:23578200-23579200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr3:23578200-23579200	Enhancers	Fetal Heart	heart
18	chr3:23578200-23580800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:23578400-23578800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:23578400-23578800	Active TSS	Brain Angular Gyrus	brain
21	chr3:23578400-23578800	Enhancers	Fetal Kidney	kidney
22	chr3:23578400-23578800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:23578400-23579000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr3:23578400-23579000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr3:23578400-23579000	Enhancers	H9 Cell Line	embryonic stem cell
26	chr3:23578400-23579000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:23578400-23579000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:23578400-23579000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:23578400-23579200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:23578400-23580800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:23578600-23578800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:23578600-23578800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:23578600-23578800	Active TSS	Brain Cingulate Gyrus	brain
34	chr3:23578600-23578800	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr3:23578600-23578800	Enhancers	Pancreas	Pancrea
36	chr3:23578600-23578800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:23578600-23579000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr3:23578600-23579000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:23578600-23579000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr3:23578600-23579200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:23578600-23579200	Enhancers	Brain Anterior Caudate	brain
42	chr3:23578600-23579200	Enhancers	Brain Germinal Matrix	brain
43	chr3:23578600-23579200	Enhancers	Brain Substantia Nigra	brain

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