Variant report

Variant	rs6771118
Chromosome Location	chr3:145782130-145782131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:145781631-145782986	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:145781500-145783077	U87	brain:	n/a	n/a
3	POLR2A	chr3:145781522-145782467	U87	brain:	n/a	n/a
4	POLR2A	chr3:145779113-145782868	A549	lung:	n/a	n/a
5	POLR2A	chr3:145782026-145782377	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:145781554-145782467	U87	brain:	n/a	n/a
7	POLR2A	chr3:145781971-145782279	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145782122..145785411-chr3:145878106..145882365,5	MCF-7	breast:
2	chr3:145779679..145784840-chr3:145877412..145880527,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243415	TF binding region
ENSG00000261051	TF binding region
ENSG00000232013	TF binding region
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10935601	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935602	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10935604	0.95[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes]
rs1170389	0.81[CHB][hapmap]
rs1170390	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1170391	0.81[CHB][hapmap]
rs1170393	0.81[CHB][hapmap]
rs11717610	0.84[EUR][1000 genomes]
rs13087364	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088180	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375580	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1375591	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1449443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449446	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16857897	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16857919	0.83[EUR][1000 genomes]
rs1707469	0.81[CHB][hapmap]
rs1868541	0.81[CHB][hapmap]
rs1982382	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762694	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792340	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792345	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804663	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804667	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611785	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681293	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681297	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56686359	0.84[EUR][1000 genomes]
rs6771106	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6775684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781300	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6783926	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792464	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794727	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7613150	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs7628805	0.82[JPT][hapmap]
rs7642940	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820945	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836725	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869137	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881772	0.80[LWK][hapmap]

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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 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	chr3:145762800-145785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:145768800-145788400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:145773800-145783600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:145774600-145787200	Weak transcription	Esophagus	oesophagus
5	chr3:145774600-145795400	Weak transcription	Aorta	Aorta
6	chr3:145775400-145786600	Weak transcription	HepG2	liver
7	chr3:145776200-145786000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:145776200-145786400	Weak transcription	Adipose Nuclei	Adipose
9	chr3:145776600-145787200	Weak transcription	HMEC	breast
10	chr3:145776800-145782400	Weak transcription	NH-A	brain
11	chr3:145776800-145783600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:145777000-145783600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:145777000-145783600	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:145777600-145783600	Strong transcription	Osteobl	bone
16	chr3:145778200-145782400	Weak transcription	HSMMtube	muscle
17	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
18	chr3:145778600-145789000	Weak transcription	Left Ventricle	heart
19	chr3:145778800-145788400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:145779000-145789600	Weak transcription	Fetal Heart	heart
21	chr3:145779400-145783000	Strong transcription	A549	lung
22	chr3:145779400-145788800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:145779600-145784200	Strong transcription	HSMM	muscle
24	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
25	chr3:145780000-145783600	Weak transcription	Fetal Lung	lung
26	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:145780200-145784200	Weak transcription	NHLF	lung
28	chr3:145780600-145784200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
30	chr3:145780800-145786600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:145780800-145793800	Weak transcription	Ovary	ovary
32	chr3:145780800-145793800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:145781000-145783600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:145781000-145788400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:145781000-145788800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:145781800-145785000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
39	chr3:145782000-145782600	Strong transcription	Liver	Liver
40	chr3:145782000-145782600	Strong transcription	Fetal Intestine Large	intestine
41	chr3:145782000-145783000	Strong transcription	HUVEC	blood vessel
42	chr3:145782000-145783200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:145782000-145785400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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