Variant report

Variant	rs17471088
Chromosome Location	chr7:27014440-27014441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10085721	0.80[CHB][hapmap]
rs10227231	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10227553	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10227673	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10238645	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10239608	0.89[CHB][hapmap]
rs10242572	0.90[JPT][hapmap]
rs10242754	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10244751	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10248684	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10256250	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10256561	0.80[CHB][hapmap]
rs10267950	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10269731	0.80[CHB][hapmap]
rs10270187	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10272190	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10272457	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10276471	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10486478	0.89[JPT][hapmap]
rs10486483	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10486485	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10951149	0.80[CHB][hapmap]
rs1123156	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs1123158	0.89[CHB][hapmap]
rs11563327	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12530718	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12532796	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12533561	0.81[ASN][1000 genomes]
rs12534899	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12534901	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534912	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535784	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12536560	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12537323	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs12540388	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1327988	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1327989	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs13438513	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs13438514	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs17315775	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs17315929	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs17323934	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs17377696	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17436410	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17471061	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030136	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2031811	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2079138	0.86[EUR][1000 genomes]
rs2082365	0.89[CHB][hapmap]
rs2248744	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2253415	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2254463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2264802	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264803	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2391360	0.89[CHB][hapmap]
rs2391362	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2428416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2428417	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2428418	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs2428421	0.87[EUR][1000 genomes]
rs2428425	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2428431	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2462900	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2462904	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2462906	0.85[EUR][1000 genomes]
rs2462908	0.88[EUR][1000 genomes]
rs2462910	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2465266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2465270	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs2465271	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465274	0.86[EUR][1000 genomes]
rs2522824	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2522825	0.84[EUR][1000 genomes]
rs2522826	0.85[EUR][1000 genomes]
rs2648076	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2693659	0.87[EUR][1000 genomes]
rs2693662	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2693665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2693668	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712234	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2712238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712242	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712244	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712245	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712246	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712248	0.86[EUR][1000 genomes]
rs2712250	1.00[AFR][1000 genomes]
rs3801803	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs3801805	0.90[JPT][hapmap]
rs3801807	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801808	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801810	0.90[JPT][hapmap]
rs3801812	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801813	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801814	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801815	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801816	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801819	0.88[JPT][hapmap]
rs3801820	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs3801821	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs3801825	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801827	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801828	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801830	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs3801840	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs3801842	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801843	0.89[CHB][hapmap]
rs3801844	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801848	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3801850	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3823932	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3823933	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs3823934	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3823936	1.00[JPT][hapmap]
rs55889667	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56144845	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62454249	0.88[ASN][1000 genomes]
rs6461979	0.90[JPT][hapmap]
rs6948657	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs7785832	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs7791513	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs7804356	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7805766	0.90[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17471088	HOXA2	cis	Whole Blood	GTEx
rs17471088	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:1 , 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

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