Variant report

Variant	rs2253415
Chromosome Location	chr7:27034947-27034948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10227231	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10227553	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10227673	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs10238645	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10242572	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10242754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10244751	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10248684	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10256250	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10270187	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10272190	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10272457	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10276471	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs10486483	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs10486485	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs11563327	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12530718	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532796	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12534899	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12534901	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12534912	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12535784	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12537323	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12540388	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs13438513	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs13438514	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs17315775	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs17315929	0.89[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs17323934	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs17377696	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17436410	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17471061	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17471088	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2030136	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2031811	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs2079138	0.84[EUR][1000 genomes]
rs2082365	0.89[CHB][hapmap]
rs2248744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2254463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2264802	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2264803	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2391362	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs2428416	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2428417	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2428418	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2428421	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2428425	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2428431	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2462900	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2462902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2462904	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462906	0.82[EUR][1000 genomes]
rs2462908	0.85[EUR][1000 genomes]
rs2462910	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2465264	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2465266	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2465270	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2465271	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2465274	0.84[EUR][1000 genomes]
rs2522824	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2522825	0.82[EUR][1000 genomes]
rs2522826	0.83[EUR][1000 genomes]
rs2648076	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2693659	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2693662	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2693665	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2693668	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2712234	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2712238	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712242	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712244	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712245	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2712246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2712248	0.83[EUR][1000 genomes]
rs3801803	0.89[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs3801805	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3801807	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs3801808	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801810	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs3801812	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801813	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801814	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801815	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801816	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801819	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs3801820	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs3801821	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3801825	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801827	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801828	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3801830	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3823932	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3823933	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3823934	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs3823936	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs55889667	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56144845	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62454249	0.86[ASN][1000 genomes]
rs6461979	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs6948657	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7785832	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7791513	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7799888	0.88[CHB][hapmap]
rs7804356	0.89[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs7805766	0.88[CHB][hapmap];0.89[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2253415	HOTAIRM1	cis	Whole Blood	GTEx
rs2253415	C7orf31	cis	parietal	SCAN
rs2253415	HOXA2	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27032200-27035000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:27033600-27035000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
3	chr7:27034000-27035600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
4	chr7:27034000-27035800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr7:27034000-27035800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr7:27034400-27036000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
7	chr7:27034600-27037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:27034800-27035800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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