Variant report

Variant	rs2712232
Chromosome Location	chr7:27088296-27088297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	7:27082525-27089724..7:27130634-27137201	Hela-S3	cervix:
2	7:27082525-27089724..7:27165488-27167947	Hela-S3	cervix:
3	7:27082525-27089724..7:27176959-27181770	Hela-S3	cervix:
4	7:27082525-27089724..7:27181770-27195105	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000105991	Chromatin interaction
ENSG00000105997	Chromatin interaction
ENSG00000106006	Chromatin interaction
ENSG00000273433	Chromatin interaction
ENSG00000106004	Chromatin interaction
ENSG00000254369	Chromatin interaction
ENSG00000272801	Chromatin interaction
ENSG00000233429	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1005977	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10231265	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10267442	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082313	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11975480	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13311400	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2015424	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs213514	0.80[ASN][1000 genomes]
rs213520	0.86[EUR][1000 genomes]
rs213532	0.81[ASN][1000 genomes]
rs2252947	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2264680	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2428420	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2428424	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2428426	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2428427	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2428428	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2428430	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462901	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2462903	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462905	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2462907	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465265	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2465267	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2522822	0.94[EUR][1000 genomes]
rs2522823	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2522829	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2693658	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2693666	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712231	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712235	0.93[EUR][1000 genomes]
rs2712240	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2712241	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712243	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2712249	0.93[EUR][1000 genomes]
rs2936426	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2960784	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2960785	0.80[ASN][1000 genomes]
rs2960786	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs774248	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs774254	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs774255	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs774264	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs774267	0.80[ASN][1000 genomes]
rs774269	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs799237	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2712232	SKAP2	cis	Whole Blood	GTEx
rs2712232	HOTAIRM1	cis	Whole Blood	GTEx
rs2712232	HOXA-AS2	cis	Whole Blood	GTEx
rs2712232	HOXA2	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27086800-27092800	Weak transcription	A549	lung
2	chr7:27086800-27092800	Weak transcription	NHDF-Ad	bronchial
3	chr7:27087200-27091000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:27087400-27092400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:27087400-27092600	Weak transcription	Hela-S3	cervix
6	chr7:27088200-27092600	Weak transcription	Osteobl	bone

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