Variant report

Variant	rs2693661
Chromosome Location	chr7:27023064-27023065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:27017279-27025474..7:27176959-27181770	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000254369	Chromatin interaction
ENSG00000105997	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10257437	0.82[CEU][hapmap]
rs10257464	0.87[CEU][hapmap]
rs10276952	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11977871	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12667139	0.92[ASN][1000 genomes]
rs12673984	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700771	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700785	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13230726	0.84[EUR][1000 genomes]
rs1560621	0.91[ASN][1000 genomes]
rs17426751	0.92[ASN][1000 genomes]
rs17426772	0.92[ASN][1000 genomes]
rs17427218	0.86[ASN][1000 genomes]
rs17436757	0.93[ASN][1000 genomes]
rs17436827	0.90[ASN][1000 genomes]
rs17437154	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs17448689	0.95[ASN][1000 genomes]
rs17448911	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs17471054	0.95[ASN][1000 genomes]
rs213516	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213520	0.80[AFR][1000 genomes]
rs2259141	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301719	0.89[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2522822	0.82[YRI][hapmap]
rs2648079	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2693660	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693669	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2936424	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936425	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62446163	0.92[ASN][1000 genomes]
rs62446164	0.92[ASN][1000 genomes]
rs62448205	0.91[ASN][1000 genomes]
rs62454246	0.88[ASN][1000 genomes]
rs62454250	0.91[ASN][1000 genomes]
rs62457399	0.93[ASN][1000 genomes]
rs62457403	0.93[ASN][1000 genomes]
rs62457404	0.82[ASN][1000 genomes]
rs6948446	0.83[ASN][1000 genomes]
rs6953314	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs706015	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs706019	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774244	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs774245	0.96[EUR][1000 genomes]
rs774249	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774250	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774251	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774252	0.82[CEU][hapmap]
rs774253	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774256	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774263	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774265	0.81[CEU][hapmap]
rs774266	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791056	0.82[CEU][hapmap]
rs813501	0.93[ASN][1000 genomes]
rs954051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv966767	chr7:27019816-27023367	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2693661	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27005800-27029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:27022400-27024400	Enhancers	Ovary	ovary

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