Variant report

Variant	rs2462901
Chromosome Location	chr7:27062849-27062850
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	7:27061277-27071265..7:27203007-27207968	H1-hESC	embryonic stem cell:	embryo
2	7:27061277-27071265..7:27238414-27242313	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000243766	Chromatin interaction
ENSG00000078399	Chromatin interaction
ENSG00000106031	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1005977	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10231265	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10267442	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1082313	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11975480	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13311400	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015424	0.93[EUR][1000 genomes]
rs2030137	0.83[ASN][1000 genomes]
rs213514	0.87[ASN][1000 genomes]
rs213520	0.87[EUR][1000 genomes]
rs213532	0.88[ASN][1000 genomes]
rs2252947	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2264680	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2428420	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2428424	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2428426	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2428427	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2428428	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2428430	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2462903	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2462905	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2462907	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2465263	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap]
rs2465265	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2465267	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2522822	0.92[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2522823	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2522829	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2693658	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2693666	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2712231	0.87[CEU][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2712232	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2712235	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2712240	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712241	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2712243	0.94[EUR][1000 genomes]
rs2712249	0.89[EUR][1000 genomes]
rs2936426	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2960784	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2960785	0.87[ASN][1000 genomes]
rs2960786	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs774248	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774254	0.92[CEU][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774255	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774264	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774267	0.90[ASN][1000 genomes]
rs774269	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs799237	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2462901	HOXA2	cis	Whole Blood	GTEx
rs2462901	HOXA-AS2	cis	Whole Blood	GTEx
rs2462901	SKAP2	cis	Whole Blood	GTEx
rs2462901	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27048200-27064400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:27062800-27063600	Enhancers	Monocytes-CD14+_RO01746	blood

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