Variant report

Variant	rs2936424
Chromosome Location	chr7:26950206-26950207
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10257437	0.82[CEU][hapmap]
rs10257464	0.87[CEU][hapmap]
rs10276952	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11977871	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12667139	0.96[ASN][1000 genomes]
rs12700771	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12700785	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1560621	0.94[ASN][1000 genomes]
rs17426751	0.96[ASN][1000 genomes]
rs17426772	0.96[ASN][1000 genomes]
rs17427218	0.85[ASN][1000 genomes]
rs17436757	0.91[ASN][1000 genomes]
rs17436827	0.88[ASN][1000 genomes]
rs17437154	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17448689	0.93[ASN][1000 genomes]
rs17448911	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17471054	0.93[ASN][1000 genomes]
rs213515	0.88[CEU][hapmap]
rs213516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213520	0.93[AFR][1000 genomes]
rs213533	0.82[CEU][hapmap]
rs213536	0.82[CEU][hapmap]
rs2259141	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301719	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs2648079	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2693660	0.86[CEU][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2693661	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2693669	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936425	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477924	0.82[CEU][hapmap]
rs591895	0.88[CEU][hapmap]
rs62446163	0.96[ASN][1000 genomes]
rs62446164	0.96[ASN][1000 genomes]
rs62448205	0.94[ASN][1000 genomes]
rs62454246	0.91[ASN][1000 genomes]
rs62454250	0.95[ASN][1000 genomes]
rs62457399	0.91[ASN][1000 genomes]
rs62457403	0.91[ASN][1000 genomes]
rs62457404	0.81[ASN][1000 genomes]
rs659131	0.81[CEU][hapmap]
rs6948446	0.82[ASN][1000 genomes]
rs706015	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs706019	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774244	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774245	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs774249	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774250	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774251	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774252	0.82[CEU][hapmap]
rs774253	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774256	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774263	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774265	0.94[CEU][hapmap]
rs774266	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7791056	0.82[CEU][hapmap]
rs813501	0.95[ASN][1000 genomes]
rs954051	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2936424	HOXA2	Cis_1M	lymphoblastoid	RTeQTL
rs2936424	HOTAIRM1	cis	Whole Blood	GTEx
rs2936424	SKAP2	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26948200-26950400	Enhancers	NHEK	skin
2	chr7:26948400-26950400	Enhancers	HMEC	breast
3	chr7:26948400-26950400	Enhancers	HUVEC	blood vessel
4	chr7:26948400-26950600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:26948400-26950800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:26948600-26950600	Enhancers	Hela-S3	cervix
7	chr7:26949000-26950400	Enhancers	A549	lung
8	chr7:26949200-26950400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:26949200-26950400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:26949400-26950400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:26949400-26950400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr7:26949400-26950400	Enhancers	HepG2	liver
13	chr7:26949400-26950600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:26949400-26950600	Enhancers	NHDF-Ad	bronchial
15	chr7:26949600-26950400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr7:26949600-26950400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:26949600-26950600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:26949600-26951200	Weak transcription	Primary B cells from cord blood	blood
19	chr7:26950000-26950400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr7:26950000-26950400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr7:26950000-26952400	Enhancers	Primary monocytes fromperipheralblood	blood

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