Variant report

Variant	rs2648079
Chromosome Location	chr7:26996402-26996403
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10257437	0.82[CEU][hapmap]
rs10257464	0.82[CEU][hapmap]
rs10276952	0.84[EUR][1000 genomes]
rs11977871	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12667139	0.95[ASN][1000 genomes]
rs12700771	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12700785	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1560621	0.93[ASN][1000 genomes]
rs17426751	0.95[ASN][1000 genomes]
rs17426772	0.95[ASN][1000 genomes]
rs17427218	0.84[ASN][1000 genomes]
rs17436757	0.91[ASN][1000 genomes]
rs17436827	0.87[ASN][1000 genomes]
rs17437154	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17448689	0.92[ASN][1000 genomes]
rs17448911	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17471054	0.92[ASN][1000 genomes]
rs213515	0.88[CEU][hapmap]
rs213516	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs213520	0.82[AFR][1000 genomes]
rs213533	0.82[CEU][hapmap]
rs213536	0.82[CEU][hapmap]
rs2259141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301719	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap]
rs2465265	0.87[YRI][hapmap]
rs2522822	0.89[YRI][hapmap]
rs2693660	0.93[CEU][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2693661	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2693669	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936424	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2936425	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs477924	0.82[CEU][hapmap]
rs591895	0.82[CEU][hapmap]
rs62446163	0.95[ASN][1000 genomes]
rs62446164	0.95[ASN][1000 genomes]
rs62448205	0.93[ASN][1000 genomes]
rs62454246	0.91[ASN][1000 genomes]
rs62454250	0.94[ASN][1000 genomes]
rs62457399	0.91[ASN][1000 genomes]
rs62457403	0.91[ASN][1000 genomes]
rs659131	0.81[CEU][hapmap]
rs6948446	0.81[ASN][1000 genomes]
rs706015	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs706019	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774244	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774245	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs774249	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774250	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774251	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774252	0.82[CEU][hapmap]
rs774253	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774256	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774263	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774265	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs774266	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7791056	0.82[CEU][hapmap]
rs813501	0.94[ASN][1000 genomes]
rs954051	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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	nsv1033272	chr7:26976426-27020206	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2648079	HOXA2	Cis_1M	lymphoblastoid	RTeQTL
rs2648079	SKAP2	cis	Whole Blood	GTEx
rs2648079	STK31	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26991200-26998000	Weak transcription	NHDF-Ad	bronchial
2	chr7:26991600-26999200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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