Variant report

Variant	rs2693662
Chromosome Location	chr7:26989564-26989565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26988409..26991338-chr7:26991544..26993555,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10227231	0.81[ASN][1000 genomes]
rs10227529	0.81[ASN][1000 genomes]
rs10227553	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227673	0.81[ASN][1000 genomes]
rs10236221	0.81[ASN][1000 genomes]
rs10238645	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10242572	0.81[ASN][1000 genomes]
rs10242754	0.82[CEU][hapmap]
rs10244751	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10248500	0.81[ASN][1000 genomes]
rs10248684	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10251839	0.81[ASN][1000 genomes]
rs10256250	0.81[ASN][1000 genomes]
rs10270187	0.81[ASN][1000 genomes]
rs10272190	0.81[ASN][1000 genomes]
rs10272457	0.81[ASN][1000 genomes]
rs10272603	0.81[ASN][1000 genomes]
rs10486483	0.81[ASN][1000 genomes]
rs10486485	0.83[ASN][1000 genomes]
rs11563327	0.83[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12530718	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533561	0.84[ASN][1000 genomes]
rs12534899	0.81[ASN][1000 genomes]
rs12534901	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534912	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534921	0.81[ASN][1000 genomes]
rs12535784	0.81[ASN][1000 genomes]
rs12536145	0.81[ASN][1000 genomes]
rs12540045	0.81[ASN][1000 genomes]
rs12540388	0.83[ASN][1000 genomes]
rs12540508	0.81[ASN][1000 genomes]
rs13438514	0.81[ASN][1000 genomes]
rs17315929	0.81[ASN][1000 genomes]
rs17323934	0.83[ASN][1000 genomes]
rs17375272	0.81[ASN][1000 genomes]
rs17376018	0.81[ASN][1000 genomes]
rs17377696	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17436410	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471061	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[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]
rs1967332	0.81[ASN][1000 genomes]
rs1982995	0.81[ASN][1000 genomes]
rs2031811	0.81[ASN][1000 genomes]
rs2248744	0.85[CEU][hapmap]
rs2253415	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2254463	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2264802	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2264803	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2391362	0.83[ASN][1000 genomes]
rs2428416	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2428417	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2428418	1.00[AFR][1000 genomes]
rs2428421	0.84[EUR][1000 genomes]
rs2462900	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462902	0.83[ASN][1000 genomes]
rs2462904	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[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	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2465266	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2465270	1.00[AFR][1000 genomes]
rs2465271	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2522824	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2648076	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693659	0.84[EUR][1000 genomes]
rs2693665	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2693668	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712234	0.89[CEU][hapmap]
rs2712238	0.89[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2712242	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712244	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712246	0.83[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[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	0.83[ASN][1000 genomes]
rs3801805	0.81[ASN][1000 genomes]
rs3801807	0.81[ASN][1000 genomes]
rs3801808	0.81[ASN][1000 genomes]
rs3801809	0.81[ASN][1000 genomes]
rs3801812	0.81[ASN][1000 genomes]
rs3801813	0.81[ASN][1000 genomes]
rs3801814	0.81[ASN][1000 genomes]
rs3801815	0.81[ASN][1000 genomes]
rs3801819	0.81[ASN][1000 genomes]
rs3823928	0.81[ASN][1000 genomes]
rs3934268	0.81[ASN][1000 genomes]
rs4719882	0.81[ASN][1000 genomes]
rs4722647	0.81[ASN][1000 genomes]
rs55889667	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56144845	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[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]
rs6461979	0.81[ASN][1000 genomes]
rs6461980	0.81[ASN][1000 genomes]
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]
rs7791513	0.81[ASN][1000 genomes]
rs7804356	0.81[ASN][1000 genomes]
rs7804620	0.81[ASN][1000 genomes]
rs7805766	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2693662	HOTAIRM1	cis	Whole Blood	GTEx
rs2693662	HOXA2	cis	Whole Blood	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26985200-26994600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:26986800-26992000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr7:26987400-26989600	Enhancers	Fetal Lung	lung
4	chr7:26987600-26989600	Enhancers	NHEK	skin
5	chr7:26987600-26989800	Enhancers	HepG2	liver
6	chr7:26987600-26992400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr7:26987800-26989600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:26988000-26989600	Enhancers	A549	lung
9	chr7:26988000-26990200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:26988400-26989600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:26988800-26989600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr7:26989000-26991400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr7:26989000-26992000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr7:26989200-26989600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr7:26989200-26990600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:26989400-26989600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr7:26989400-26990400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:26989400-26991600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr7:26989400-26992400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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