Variant report

Variant	rs2712249
Chromosome Location	chr7:27119517-27119518
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	chr7:27116970..27119850-chr7:27128601..27130256,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1005977	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10231265	0.93[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs10267442	0.90[EUR][1000 genomes]
rs1082313	0.81[EUR][1000 genomes]
rs11975480	0.88[EUR][1000 genomes]
rs12673984	0.92[AFR][1000 genomes]
rs12700785	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs2015424	0.92[EUR][1000 genomes]
rs2252947	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs2264680	0.86[EUR][1000 genomes]
rs2428420	0.89[EUR][1000 genomes]
rs2428424	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2428426	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2428427	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2428428	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2428430	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs2462901	0.92[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs2462903	0.89[EUR][1000 genomes]
rs2462905	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462907	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2465263	1.00[CEU][hapmap]
rs2465265	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2465267	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2522822	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2522823	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs2522829	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs2693658	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2693666	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs2712231	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2712232	0.93[EUR][1000 genomes]
rs2712235	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712240	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2712241	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs2712243	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953314	0.92[AFR][1000 genomes]
rs774248	0.80[EUR][1000 genomes]
rs774254	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs774255	0.96[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs774264	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs799237	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[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	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
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv887856	chr7:27073731-27297791	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
6	nsv824038	chr7:27119294-27284522	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2712249	HOXA-AS2	cis	Whole Blood	GTEx
rs2712249	SKAP2	cis	Whole Blood	GTEx
rs2712249	HOXA2	cis	Whole Blood	GTEx
rs2712249	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27118400-27119600	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr7:27118400-27120000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:27118400-27120400	Enhancers	NHEK	skin
4	chr7:27118400-27122600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:27118600-27119800	Enhancers	Fetal Intestine Large	intestine
6	chr7:27118600-27119800	Enhancers	A549	lung
7	chr7:27118800-27121400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:27118800-27122600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:27118800-27122800	Enhancers	HMEC	breast
10	chr7:27119000-27119600	Enhancers	GM12878-XiMat	blood
11	chr7:27119000-27120400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:27119000-27122600	Enhancers	Hela-S3	cervix
13	chr7:27119200-27120400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:27119200-27121000	Enhancers	HepG2	liver
15	chr7:27119200-27121800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:27119200-27127600	Weak transcription	Osteobl	bone
17	chr7:27119400-27120000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr7:27119400-27120600	Weak transcription	Fetal Intestine Small	intestine
19	chr7:27119400-27121000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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