Variant report

Variant	rs12643627
Chromosome Location	chr4:8609195-8609196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8607464..8609784-chr4:8610863..8613633,2	MCF-7	breast:
2	chr4:8595503..8598248-chr4:8607204..8609791,3	MCF-7	breast:
3	chr4:8594040..8595789-chr4:8608077..8610422,2	MCF-7	breast:
4	chr4:8604553..8606540-chr4:8607081..8609786,2	MCF-7	breast:
5	chr4:8609002..8610016-chr4:8919155..8920078,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109625	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12648807	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12650877	0.91[ASN][1000 genomes]
rs2302568	0.91[ASN][1000 genomes]
rs3796737	0.84[EUR][1000 genomes]
rs3796739	0.84[EUR][1000 genomes]
rs4302446	0.89[ASN][1000 genomes]
rs6834153	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6852449	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73213364	0.84[EUR][1000 genomes]
rs73213381	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73213401	0.91[ASN][1000 genomes]
rs73215205	0.82[ASN][1000 genomes]
rs7692629	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv878612	chr4:8534283-8618916	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1832730	chr4:8541086-9514568	Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
5	esv1843578	chr4:8541086-9514568	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv878613	chr4:8554894-8618916	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv878614	chr4:8554894-8669619	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv878615	chr4:8566758-8625245	Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv878616	chr4:8566758-8669619	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv878617	chr4:8566758-9371116	ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	nsv1014219	chr4:8578779-8724531	Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv878618	chr4:8579758-8641696	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv878619	chr4:8579758-8669619	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv878620	chr4:8584879-8674871	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv470015	chr4:8584879-8729638	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv878621	chr4:8584879-9371116	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
17	nsv878622	chr4:8599250-9371116	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
18	nsv829855	chr4:8604879-8729607	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv915590	chr4:8607839-9558139	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
20	nsv521867	chr4:8608066-8641696	Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8573400-8609400	Weak transcription	Right Atrium	heart
2	chr4:8596000-8622800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:8596000-8623200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:8597600-8618400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:8599600-8616000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:8601200-8611400	Weak transcription	Spleen	Spleen
7	chr4:8601400-8616000	Weak transcription	HSMMtube	muscle
8	chr4:8601600-8609600	Strong transcription	Ovary	ovary
9	chr4:8601600-8620200	Weak transcription	NHDF-Ad	bronchial
10	chr4:8601800-8617000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:8601800-8622000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:8603200-8609200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:8603200-8615400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:8605800-8612000	Weak transcription	Gastric	stomach
15	chr4:8606800-8615400	Weak transcription	Osteobl	bone
16	chr4:8607800-8616000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:8608000-8610200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:8608000-8613000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:8608200-8610400	Genic enhancers	Placenta	Placenta
20	chr4:8608400-8614200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:8609000-8609200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:8609000-8609200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr4:8609000-8609200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:8609000-8609400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
25	chr4:8609000-8609600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:8609000-8610200	Genic enhancers	H1 Cell Line	embryonic stem cell

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