Variant report

Variant	rs7776505
Chromosome Location	chr7:27034151-27034152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10081212	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10242380	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10257437	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10257464	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10259208	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10267689	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1082312	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1082315	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11974418	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11977871	0.82[CEU][hapmap]
rs12700785	0.82[CEU][hapmap]
rs13221446	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17500459	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1874924	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs213515	0.93[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs213516	0.82[CEU][hapmap]
rs213518	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs213521	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs213533	0.88[CEU][hapmap]
rs213536	0.88[CEU][hapmap]
rs2140998	0.93[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2693661	0.82[CEU][hapmap]
rs2936423	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34889704	0.87[AMR][1000 genomes]
rs477924	0.88[CEU][hapmap]
rs591895	0.87[CEU][hapmap]
rs6461982	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs659131	0.87[CEU][hapmap]
rs6974705	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs774246	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs774247	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs774252	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs774253	0.82[CEU][hapmap]
rs774257	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs774258	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs774259	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs774260	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs774261	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs774262	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs774265	0.93[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs774268	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7791056	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7797624	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs954051	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7776505	HOXA2	Cis_1M	lymphoblastoid	RTeQTL
rs7776505	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27032000-27034600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr7:27032200-27034400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:27032200-27034600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:27032200-27034600	Enhancers	HMEC	breast
5	chr7:27032200-27034600	Enhancers	NHEK	skin
6	chr7:27032200-27035000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:27032800-27034200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:27033200-27034200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:27033200-27034200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:27033600-27035000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr7:27033800-27034200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:27033800-27034200	Enhancers	Fetal Lung	lung
13	chr7:27034000-27034200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
14	chr7:27034000-27034200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr7:27034000-27035600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
16	chr7:27034000-27035800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr7:27034000-27035800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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