Variant report

Variant	rs5012709
Chromosome Location	chr4:7950862-7950863
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7940858..7944255-chr4:7948731..7952415,4	MCF-7	breast:
2	chr4:7948820..7951616-chr4:7956556..7958489,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11940122	0.81[CEU][hapmap]
rs12641498	0.92[JPT][hapmap]
rs13139805	0.93[JPT][hapmap]
rs1317111	1.00[JPT][hapmap]
rs1320069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1320070	1.00[JPT][hapmap]
rs1320071	1.00[JPT][hapmap]
rs1320074	0.92[JPT][hapmap]
rs13435730	1.00[JPT][hapmap]
rs16841417	1.00[YRI][hapmap]
rs17770447	0.93[JPT][hapmap]
rs17833038	0.93[JPT][hapmap]
rs1814873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1814874	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2385902	0.93[JPT][hapmap]
rs2385911	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385913	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2386056	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4235268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4385040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696778	0.92[JPT][hapmap]
rs4696779	0.93[JPT][hapmap]
rs4696825	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696827	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447871	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816560	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6819776	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6848540	0.93[JPT][hapmap]
rs7437940	0.92[JPT][hapmap]
rs7437984	0.93[JPT][hapmap]
rs7655226	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667982	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7681378	0.88[ASN][1000 genomes]
rs7683285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7685634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938604	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv593621	chr4:7943106-7969594	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv20550	chr4:7950857-7951577	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7941600-7951200	Weak transcription	Small Intestine	intestine
2	chr4:7942000-7951000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:7942000-7951400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:7945400-7957400	Weak transcription	Placenta	Placenta
5	chr4:7948400-7951000	Weak transcription	Fetal Brain Female	brain
6	chr4:7948600-7951000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:7949000-7952400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:7949800-7951600	Enhancers	Fetal Brain Male	brain
9	chr4:7950000-7951200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:7950400-7951200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:7950400-7951400	Enhancers	Pancreas	Pancrea
12	chr4:7950400-7951600	Enhancers	Duodenum Mucosa	Duodenum
13	chr4:7950400-7951800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:7950400-7951800	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr4:7950400-7951800	Enhancers	Fetal Intestine Large	intestine
16	chr4:7950400-7951800	Enhancers	Fetal Intestine Small	intestine
17	chr4:7950600-7951200	Enhancers	Ovary	ovary
18	chr4:7950600-7951200	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr4:7950600-7951200	Enhancers	Osteobl	bone
20	chr4:7950600-7951600	Enhancers	Colon Smooth Muscle	Colon
21	chr4:7950600-7951600	Enhancers	Rectal Smooth Muscle	rectum
22	chr4:7950600-7952000	Enhancers	Stomach Mucosa	stomach
23	chr4:7950600-7952600	Bivalent Enhancer	HepG2	liver
24	chr4:7950800-7951000	Enhancers	Fetal Heart	heart
25	chr4:7950800-7951400	Enhancers	Liver	Liver

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