Variant report

Variant	rs9288008
Chromosome Location	chr2:178545934-178545935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178540518..178542600-chr2:178544661..178547619,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128655	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10497498	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11891283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527405	0.93[JPT][hapmap]
rs1527408	0.93[JPT][hapmap]
rs16865443	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs16865444	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs16865446	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs16865448	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs16865449	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs16865453	0.82[CHB][hapmap]
rs16865475	0.82[JPT][hapmap]
rs16865524	0.93[JPT][hapmap]
rs2293472	0.82[JPT][hapmap]
rs2293473	0.82[JPT][hapmap]
rs2695317	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3731803	0.82[JPT][hapmap]
rs3731804	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3731806	0.82[JPT][hapmap]
rs3770018	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770019	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770020	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770022	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]
rs3821003	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3821004	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3821005	0.82[JPT][hapmap]
rs57538850	0.83[ASN][1000 genomes]
rs59259791	0.81[AFR][1000 genomes]
rs60295960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433691	0.88[CEU][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs6718206	0.94[EUR][1000 genomes]
rs6746845	0.93[JPT][hapmap]
rs73979516	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979519	0.84[AFR][1000 genomes]
rs7562940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677333	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9677970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv870023	chr2:178545623-178581407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3433715	chr2:178545654-178545959	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178536600-178556000	Weak transcription	Pancreas	Pancrea
2	chr2:178540000-178547400	Enhancers	Fetal Kidney	kidney
3	chr2:178543400-178546400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr2:178544000-178548000	Enhancers	K562	blood
5	chr2:178544600-178546800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:178544600-178552600	Weak transcription	Fetal Intestine Small	intestine
7	chr2:178545000-178547000	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:178545200-178546200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:178545200-178548000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:178545400-178546200	Weak transcription	Small Intestine	intestine
11	chr2:178545400-178549200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:178545800-178546600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:178545800-178547400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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