Variant report

Variant	rs2960785
Chromosome Location	chr7:26952139-26952140
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	chr7:26951086..26952616-chr7:26955450..26957665,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10231265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10267442	0.80[ASN][1000 genomes]
rs1082313	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11975480	0.80[ASN][1000 genomes]
rs13311400	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213514	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs213520	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs213527	0.82[LWK][hapmap]
rs213532	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2252947	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[ASN][1000 genomes]
rs2264680	0.92[ASN][1000 genomes]
rs2428420	0.89[ASN][1000 genomes]
rs2428430	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[ASN][1000 genomes]
rs2462901	0.90[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs2462907	0.91[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap]
rs2465263	0.91[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap]
rs2465265	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2465267	0.80[CEU][hapmap]
rs2522822	0.90[JPT][hapmap]
rs2522823	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs2522829	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs2693666	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[ASN][1000 genomes]
rs2712231	0.80[ASN][1000 genomes]
rs2712232	0.80[ASN][1000 genomes]
rs2712241	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2769364	0.84[CEU][hapmap]
rs2769365	0.81[CEU][hapmap]
rs2936426	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960784	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960786	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801806	0.85[CEU][hapmap]
rs3807592	0.82[CHB][hapmap]
rs503110	0.85[CEU][hapmap]
rs570840	0.84[CEU][hapmap]
rs607099	0.85[CEU][hapmap]
rs667841	0.83[CEU][hapmap]
rs71521786	0.87[ASN][1000 genomes]
rs774245	0.84[AFR][1000 genomes]
rs774248	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774254	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs774255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs774264	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774267	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774269	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs799237	0.91[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2960785	SKAP2	cis	Whole Blood	GTEx
rs2960785	HOTAIRM1	cis	Whole Blood	GTEx
rs2960785	C7orf31	cis	parietal	SCAN
rs2960785	HOXA3	cis	Whole Blood	GTEx
rs2960785	HOXA-AS2	cis	Whole Blood	GTEx
rs2960785	HOXA2	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26950000-26952400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr7:26950400-26952200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:26950400-26956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:26950400-26957400	Weak transcription	NHEK	skin
5	chr7:26950400-26957600	Weak transcription	HMEC	breast
6	chr7:26950600-26958000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:26950600-26958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:26951200-26952400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr7:26951200-26952600	Enhancers	Primary B cells from cord blood	blood
10	chr7:26951600-26952400	Enhancers	HepG2	liver
11	chr7:26951600-26953000	Enhancers	Fetal Lung	lung
12	chr7:26951600-26953000	Enhancers	Hela-S3	cervix
13	chr7:26951800-26952200	Active TSS	Fetal Brain Male	brain
14	chr7:26951800-26952400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr7:26951800-26953400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:26952000-26952400	Enhancers	Fetal Stomach	stomach
17	chr7:26952000-26952800	Enhancers	Adipose Nuclei	Adipose
18	chr7:26952000-26953600	Enhancers	Primary neutrophils fromperipheralblood	blood

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