Variant report

Variant	rs2055307
Chromosome Location	chr3:23542254-23542255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10510539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11129120	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]
rs11706875	0.95[ASN][1000 genomes]
rs11712991	1.00[ASN][1000 genomes]
rs11713090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715736	0.86[AMR][1000 genomes];0.96[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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13316118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13323077	0.85[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1391756	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498810	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1498812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1692619	0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs1692621	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1692646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692647	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs1692648	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692649	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]
rs1695180	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs1695183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695192	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1695197	0.91[AMR][1000 genomes];0.98[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];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs17013425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17194751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.96[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	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995174	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995175	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2036044	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs2036045	0.91[YRI][hapmap]
rs2055155	1.00[YRI][hapmap]
rs2173057	0.94[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap]
rs2359761	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs28367247	1.00[ASN][1000 genomes]
rs4858070	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs4858495	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs4858499	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs4858507	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs4858517	0.95[ASN][1000 genomes]
rs56034809	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58130044	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58618629	0.95[ASN][1000 genomes]
rs58718028	0.83[EUR][1000 genomes]
rs59012069	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60028742	0.98[ASN][1000 genomes]
rs60137984	1.00[ASN][1000 genomes]
rs62255784	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255785	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255789	0.89[AMR][1000 genomes];0.96[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	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs66864142	0.81[AFR][1000 genomes];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];1.00[YRI][hapmap]
rs6807859	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68093882	1.00[ASN][1000 genomes]
rs73139773	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140507	0.94[ASN][1000 genomes]
rs73140523	0.98[ASN][1000 genomes]
rs73140544	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629327	0.91[YRI][hapmap]
rs7636705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643705	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs7646541	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7648425	1.00[YRI][hapmap]
rs778463	0.94[CEU][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs778465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[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];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778491	0.83[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];1.00[CHD][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];1.00[YRI][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];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778512	0.85[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];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778515	0.85[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs778516	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778524	0.85[CEU][hapmap]
rs778525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801277	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs809640	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931609	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs9631541	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs9757330	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs9758590	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs9848331	1.00[YRI][hapmap]
rs9862734	0.85[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.86[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2055307	ZNF385D	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23523600-23542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:23526600-23554000	Weak transcription	Primary T cells from cord blood	blood
3	chr3:23528600-23552200	Weak transcription	Ovary	ovary
4	chr3:23532200-23547800	Weak transcription	NHLF	lung
5	chr3:23536600-23557200	Weak transcription	Left Ventricle	heart
6	chr3:23537400-23542400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:23537400-23542400	Weak transcription	HMEC	breast
8	chr3:23537400-23542600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:23537400-23542600	Weak transcription	HSMM	muscle
10	chr3:23537400-23542800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:23537400-23543000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:23537400-23551400	Weak transcription	Adipose Nuclei	Adipose
13	chr3:23537400-23559400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:23537600-23542600	Weak transcription	NHEK	skin
15	chr3:23537600-23542800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:23537600-23542800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:23537600-23542800	Weak transcription	Osteobl	bone
18	chr3:23537800-23542600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:23537800-23542800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:23539400-23542400	Weak transcription	HSMMtube	muscle
21	chr3:23539600-23550000	Weak transcription	GM12878-XiMat	blood
22	chr3:23540400-23560200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:23540800-23542400	Weak transcription	Aorta	Aorta
24	chr3:23541400-23543200	Enhancers	Psoas Muscle	Psoas
25	chr3:23542000-23542400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:23542200-23542400	Enhancers	Right Ventricle	heart
27	chr3:23542200-23542800	Genic enhancers	Brain Substantia Nigra	brain
28	chr3:23542200-23543000	Flanking Active TSS	Fetal Heart	heart
29	chr3:23542200-23543200	Enhancers	Fetal Muscle Leg	muscle
30	chr3:23542200-23543400	Strong transcription	Primary B cells from cord blood	blood
31	chr3:23542200-23544000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:23542200-23544200	Enhancers	Skeletal Muscle Male	skeletal muscle

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