Variant report

Variant	rs6778577
Chromosome Location	chr3:23988009-23988010
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23849969..23852479-chr3:23986397..23988332,3	K562	blood:
2	chr3:23846531..23848270-chr3:23987055..23988984,2	MCF-7	breast:
3	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
4	chr3:23986158..23988420-chr3:24004373..24006448,3	MCF-7	breast:
5	chr3:23987103..23988093-chr6:56911476..56911991,2	Hela-S3	cervix:
6	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
7	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174738	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000168116	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10084748	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1037635	0.83[MEX][hapmap]
rs10865791	0.83[YRI][hapmap]
rs11129128	0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13087250	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13316457	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13317815	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321439	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321440	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533141	0.85[EUR][1000 genomes]
rs1567579	0.90[EUR][1000 genomes]
rs1567580	0.90[EUR][1000 genomes]
rs2360020	0.87[ASN][1000 genomes]
rs28524116	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34036067	0.81[EUR][1000 genomes]
rs34058540	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34082882	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34593533	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34866549	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35136361	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35457462	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35755171	0.82[EUR][1000 genomes]
rs35755253	0.82[EUR][1000 genomes]
rs36063721	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36089963	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3762775	0.93[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs3811714	0.85[CHB][hapmap]
rs3935253	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4078155	0.83[YRI][hapmap]
rs4131404	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4132595	0.93[ASN][1000 genomes]
rs4292186	0.83[YRI][hapmap]
rs4293661	0.83[YRI][hapmap]
rs4300960	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4490300	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4578971	0.83[YRI][hapmap]
rs4602333	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4858096	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4858102	0.82[CHB][hapmap]
rs4858561	0.83[YRI][hapmap]
rs4858564	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59090179	0.83[ASN][1000 genomes]
rs6550808	0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs66609380	0.85[EUR][1000 genomes]
rs67465878	0.83[ASN][1000 genomes]
rs67606949	0.83[EUR][1000 genomes]
rs6770052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790140	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6791805	0.83[MEX][hapmap]
rs6803587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324126	0.85[EUR][1000 genomes]
rs72627028	0.80[ASN][1000 genomes]
rs72627029	0.80[ASN][1000 genomes]
rs72627030	0.80[ASN][1000 genomes]
rs72627031	0.80[ASN][1000 genomes]
rs72627032	0.80[ASN][1000 genomes]
rs72627033	0.80[ASN][1000 genomes]
rs72627034	0.80[ASN][1000 genomes]
rs72627035	0.80[ASN][1000 genomes]
rs72627036	0.80[ASN][1000 genomes]
rs72627037	0.80[ASN][1000 genomes]
rs72627038	0.80[ASN][1000 genomes]
rs72627039	0.80[ASN][1000 genomes]
rs72627040	0.80[ASN][1000 genomes]
rs72627043	0.80[ASN][1000 genomes]
rs72627044	0.87[ASN][1000 genomes]
rs72627046	0.87[ASN][1000 genomes]
rs72627047	0.83[ASN][1000 genomes]
rs72627048	0.83[ASN][1000 genomes]
rs72627049	0.83[ASN][1000 genomes]
rs72627050	0.83[ASN][1000 genomes]
rs72627051	0.87[ASN][1000 genomes]
rs72627052	0.87[ASN][1000 genomes]
rs72627053	0.87[ASN][1000 genomes]
rs72627055	0.87[ASN][1000 genomes]
rs72627056	0.87[ASN][1000 genomes]
rs72627057	0.87[ASN][1000 genomes]
rs72627058	0.87[ASN][1000 genomes]
rs72627059	0.87[ASN][1000 genomes]
rs72627060	0.87[ASN][1000 genomes]
rs72627061	0.87[ASN][1000 genomes]
rs72627062	0.87[ASN][1000 genomes]
rs72627063	0.87[ASN][1000 genomes]
rs72627064	0.87[ASN][1000 genomes]
rs72627065	0.87[ASN][1000 genomes]
rs72627067	0.87[ASN][1000 genomes]
rs72627068	0.87[ASN][1000 genomes]
rs72627069	0.87[ASN][1000 genomes]
rs72627070	0.87[ASN][1000 genomes]
rs72627071	0.87[ASN][1000 genomes]
rs72627072	0.87[ASN][1000 genomes]
rs72627073	0.87[ASN][1000 genomes]
rs72627074	0.87[ASN][1000 genomes]
rs72627075	0.87[ASN][1000 genomes]
rs72627076	0.87[ASN][1000 genomes]
rs72627078	0.86[ASN][1000 genomes]
rs72627079	0.87[ASN][1000 genomes]
rs72627080	0.87[ASN][1000 genomes]
rs72627081	0.87[ASN][1000 genomes]
rs72627082	0.87[ASN][1000 genomes]
rs72627083	0.87[ASN][1000 genomes]
rs72627084	0.87[ASN][1000 genomes]
rs72627085	0.87[ASN][1000 genomes]
rs72627086	0.87[ASN][1000 genomes]
rs72627087	0.87[ASN][1000 genomes]
rs72627088	0.87[ASN][1000 genomes]
rs72627089	0.87[ASN][1000 genomes]
rs72627090	0.87[ASN][1000 genomes]
rs72627091	0.90[ASN][1000 genomes]
rs72627094	0.94[AMR][1000 genomes]
rs72627096	0.97[ASN][1000 genomes]
rs72627097	0.97[ASN][1000 genomes]
rs72627098	0.97[ASN][1000 genomes]
rs72627099	0.97[ASN][1000 genomes]
rs72627100	0.90[ASN][1000 genomes]
rs72627101	0.90[ASN][1000 genomes]
rs72627102	0.90[ASN][1000 genomes]
rs72628103	0.90[ASN][1000 genomes]
rs72628104	0.90[ASN][1000 genomes]
rs72628105	0.90[ASN][1000 genomes]
rs72628106	0.90[ASN][1000 genomes]
rs72628107	0.90[ASN][1000 genomes]
rs72628108	0.90[ASN][1000 genomes]
rs72628109	0.90[ASN][1000 genomes]
rs72628111	0.90[ASN][1000 genomes]
rs72628112	0.87[ASN][1000 genomes]
rs72628113	0.87[ASN][1000 genomes]
rs72628114	0.87[ASN][1000 genomes]
rs72628115	0.87[ASN][1000 genomes]
rs72628116	0.87[ASN][1000 genomes]
rs72628119	0.83[ASN][1000 genomes]
rs72628123	0.83[ASN][1000 genomes]
rs72628124	0.83[ASN][1000 genomes]
rs72628126	0.87[ASN][1000 genomes]
rs73150266	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73150299	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7611018	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs7646930	0.83[YRI][hapmap]
rs954748	0.92[EUR][1000 genomes]
rs9809225	0.89[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9812419	0.83[MEX][hapmap]
rs9812870	0.81[EUR][1000 genomes]
rs9817923	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831760	0.83[YRI][hapmap]
rs9853954	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9855481	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9859567	0.80[CEU][hapmap]
rs9863123	0.85[CHB][hapmap]
rs9863176	0.83[EUR][1000 genomes]
rs9875577	0.80[CEU][hapmap];0.82[YRI][hapmap]
rs9883834	0.93[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv3449153	chr3:23984948-23988646	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3406325	chr3:23985473-23988321	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3425301	chr3:23985548-23988496	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23985600-23988200	Active TSS	Fetal Kidney	kidney
2	chr3:23985600-23988400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:23985600-23988800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:23985800-23988200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:23985800-23988200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:23985800-23988200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:23985800-23988200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr3:23985800-23988200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:23985800-23988200	Active TSS	Lung	lung
10	chr3:23985800-23988400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:23985800-23988400	Active TSS	Fetal Brain Female	brain
12	chr3:23985800-23988400	Active TSS	Psoas Muscle	Psoas
13	chr3:23985800-23988600	Active TSS	Brain Anterior Caudate	brain
14	chr3:23985800-23988800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:23986000-23988200	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:23986000-23988200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:23986000-23988200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:23986000-23988200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:23986000-23988200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:23986000-23988200	Active TSS	Colon Smooth Muscle	Colon
21	chr3:23986000-23988200	Active TSS	Placenta Amnion	Placenta Amnion
22	chr3:23986000-23988400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:23986000-23988400	Active TSS	Right Ventricle	heart
24	chr3:23986000-23988600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:23986000-23988600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:23986000-23988600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr3:23986000-23988800	Active TSS	Aorta	Aorta
28	chr3:23986000-23988800	Active TSS	Ovary	ovary
29	chr3:23986200-23988200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:23986200-23988200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:23986200-23988200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:23986200-23988200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:23986200-23988200	Active TSS	Brain Cingulate Gyrus	brain
34	chr3:23986200-23988200	Active TSS	Brain Germinal Matrix	brain
35	chr3:23986200-23988200	Active TSS	Esophagus	oesophagus
36	chr3:23986200-23988200	Active TSS	Fetal Intestine Large	intestine
37	chr3:23986200-23988200	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr3:23986200-23988200	Active TSS	Placenta	Placenta
39	chr3:23986200-23988200	Active TSS	Fetal Stomach	stomach
40	chr3:23986200-23988200	Active TSS	Pancreas	Pancrea
41	chr3:23986200-23988200	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr3:23986200-23988200	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr3:23986200-23988200	Active TSS	Small Intestine	intestine
44	chr3:23986200-23988200	Active TSS	NHDF-Ad	bronchial
45	chr3:23986200-23988600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:23986200-23988600	Active TSS	Rectal Smooth Muscle	rectum
47	chr3:23986200-23988600	Active TSS	GM12878-XiMat	blood
48	chr3:23986200-23988800	Active TSS	H1 Cell Line	embryonic stem cell
49	chr3:23986200-23988800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:23986200-23988800	Active TSS	Stomach Smooth Muscle	stomach

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