Variant report

Variant	rs2712242
Chromosome Location	chr7:26960011-26960012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26959744..26961446-chr7:26966298..26968105,2	K562	blood:

Extended variants
information (count: 208 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:206)

rs_ID	r²[population]
rs10085721	1.00[CHB][hapmap]
rs10227140	1.00[CHB][hapmap]
rs10227231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10227529	0.81[ASN][1000 genomes]
rs10227553	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10227898	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10236221	0.81[ASN][1000 genomes]
rs10238645	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10239608	1.00[CHB][hapmap]
rs10242572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10242754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10244751	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10248500	0.81[ASN][1000 genomes]
rs10248684	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10251839	0.81[ASN][1000 genomes]
rs10256250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10256561	1.00[CHB][hapmap]
rs10256799	0.89[CHB][hapmap]
rs10261915	1.00[CHB][hapmap]
rs10267950	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10269731	1.00[CHB][hapmap]
rs10270187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10272190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10272457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10272603	0.81[ASN][1000 genomes]
rs10273468	1.00[CHB][hapmap]
rs10276471	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10281261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10486478	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10486483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10486485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10951145	0.89[CHB][hapmap]
rs10951149	1.00[CHB][hapmap]
rs1123156	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1123157	1.00[CHB][hapmap]
rs1123158	1.00[CHB][hapmap]
rs11563327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11770043	1.00[CHB][hapmap]
rs11772673	1.00[CHB][hapmap]
rs11773029	1.00[CHB][hapmap]
rs12530718	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532796	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12533561	0.84[ASN][1000 genomes]
rs12534899	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12534901	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534912	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534921	0.81[ASN][1000 genomes]
rs12535784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12536145	0.81[ASN][1000 genomes]
rs12536560	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12537323	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12540045	0.81[ASN][1000 genomes]
rs12540388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12540508	0.81[ASN][1000 genomes]
rs12700755	1.00[CHB][hapmap]
rs12700759	1.00[CHB][hapmap]
rs12700761	1.00[CHB][hapmap]
rs13229947	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13234201	0.89[CHB][hapmap]
rs13234336	1.00[CHB][hapmap]
rs1327988	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1327989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13438513	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13438514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1468203	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1548478	1.00[CHB][hapmap]
rs1548479	1.00[CHB][hapmap]
rs1548481	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17315775	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17315929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17323934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17372780	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17375272	0.81[ASN][1000 genomes]
rs17376018	0.81[ASN][1000 genomes]
rs17377696	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17436410	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471061	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17471088	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859101	1.00[CHB][hapmap]
rs1967332	0.81[ASN][1000 genomes]
rs1982995	0.81[ASN][1000 genomes]
rs2023819	1.00[CHB][hapmap]
rs2030136	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2031811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2082365	1.00[CHB][hapmap]
rs2106905	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2189016	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2189017	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2189019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2248744	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2253415	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]
rs2254463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2264802	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2264803	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2391360	1.00[CHB][hapmap]
rs2391362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2428416	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2428417	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2428418	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs2428421	0.81[EUR][1000 genomes]
rs2428431	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2462900	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2462904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2462910	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465264	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2465266	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2465270	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs2465271	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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];0.86[TSI][hapmap];1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2648076	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693659	0.81[EUR][1000 genomes]
rs2693662	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693665	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693668	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712234	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2712238	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2712244	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712245	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712246	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2712250	1.00[AFR][1000 genomes]
rs28550029	0.81[ASN][1000 genomes]
rs28816386	0.81[ASN][1000 genomes]
rs28883078	0.81[ASN][1000 genomes]
rs3213853	0.81[ASN][1000 genomes]
rs3801803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3801805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801809	0.81[ASN][1000 genomes]
rs3801810	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801816	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801827	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801828	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801830	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801843	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs3801844	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801846	0.89[CHB][hapmap]
rs3801848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801850	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3801853	1.00[CHB][hapmap]
rs3801857	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs3801860	1.00[CHB][hapmap]
rs3801864	1.00[CHB][hapmap]
rs3823928	0.81[ASN][1000 genomes]
rs3823932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3823933	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3823934	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3823936	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3934268	0.81[ASN][1000 genomes]
rs4719882	0.81[ASN][1000 genomes]
rs4722630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4722631	1.00[CHB][hapmap]
rs4722647	0.81[ASN][1000 genomes]
rs5012512	0.89[CHB][hapmap]
rs55889667	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56144845	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56154570	0.81[ASN][1000 genomes]
rs57623217	0.81[ASN][1000 genomes]
rs59254259	0.81[ASN][1000 genomes]
rs61354389	0.81[ASN][1000 genomes]
rs62454249	0.91[ASN][1000 genomes]
rs6461963	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6461964	1.00[CHB][hapmap]
rs6461965	1.00[CHB][hapmap]
rs6461971	1.00[CHB][hapmap]
rs6461979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6461980	0.81[ASN][1000 genomes]
rs6948657	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6964094	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6970591	1.00[CHB][hapmap]
rs6971397	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6973237	1.00[CHB][hapmap]
rs727449	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs727450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73069507	0.81[ASN][1000 genomes]
rs73069510	0.81[ASN][1000 genomes]
rs73069533	0.81[ASN][1000 genomes]
rs73069540	0.83[ASN][1000 genomes]
rs73069541	0.83[ASN][1000 genomes]
rs7457076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs763616	1.00[CHB][hapmap]
rs7785832	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7791513	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7799888	1.00[CHB][hapmap]
rs7803699	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7804356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7804620	0.81[ASN][1000 genomes]
rs7805766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7807640	1.00[CHB][hapmap]
rs7810109	1.00[CHB][hapmap]
rs7810127	1.00[CHB][hapmap]
rs891876	1.00[CHB][hapmap]
rs9648020	1.00[CHB][hapmap]
rs989250	1.00[CHB][hapmap]

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
rs2712242	HOTAIRM1	cis	Whole Blood	GTEx
rs2712242	C7orf31	cis	parietal	SCAN
rs2712242	HOXA2	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26956000-26961400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:26957000-26962200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:26957400-26960400	Enhancers	NHEK	skin
4	chr7:26957400-26962400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr7:26957600-26960400	Enhancers	HMEC	breast
6	chr7:26958400-26960800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:26958800-26960400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr7:26959200-26960200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr7:26959200-26960800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr7:26959400-26960200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr7:26959400-26960200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr7:26959400-26960200	Enhancers	Rectal Smooth Muscle	rectum
13	chr7:26959600-26960400	Enhancers	Stomach Mucosa	stomach

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