Variant report

Variant	rs2769365
Chromosome Location	chr7:26844616-26844617
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	chr7:26843884..26846440-chr7:26852845..26855435,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10085721	0.83[JPT][hapmap]
rs10227140	0.92[JPT][hapmap]
rs10231161	0.91[JPT][hapmap]
rs10239608	0.81[JPT][hapmap]
rs10256561	0.83[JPT][hapmap]
rs10256799	0.92[JPT][hapmap]
rs10261915	0.92[JPT][hapmap]
rs10269731	0.83[JPT][hapmap]
rs10273468	0.83[JPT][hapmap]
rs10951145	1.00[JPT][hapmap]
rs10951149	0.92[JPT][hapmap]
rs1123157	0.92[JPT][hapmap]
rs1123158	0.91[JPT][hapmap]
rs11770043	0.91[JPT][hapmap]
rs11772673	0.82[JPT][hapmap]
rs11773029	0.91[JPT][hapmap]
rs12700755	0.92[JPT][hapmap]
rs12700759	0.92[JPT][hapmap]
rs12700761	0.91[JPT][hapmap]
rs13186	0.91[JPT][hapmap]
rs13234336	0.83[JPT][hapmap]
rs1548478	0.92[JPT][hapmap]
rs1548479	0.92[JPT][hapmap]
rs1859101	0.92[JPT][hapmap]
rs2023819	0.92[JPT][hapmap]
rs2082365	0.82[JPT][hapmap]
rs212842	0.91[JPT][hapmap]
rs212844	0.92[JPT][hapmap]
rs212846	0.92[JPT][hapmap]
rs212847	0.91[JPT][hapmap]
rs212852	0.91[JPT][hapmap]
rs212853	0.91[JPT][hapmap]
rs212858	0.92[JPT][hapmap]
rs213527	0.82[CEU][hapmap]
rs2237328	0.92[JPT][hapmap]
rs2282906	0.91[JPT][hapmap]
rs2299102	0.91[JPT][hapmap]
rs2391360	0.91[JPT][hapmap]
rs2769364	0.96[CEU][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34833677	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3801806	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3801835	0.90[ASN][1000 genomes]
rs3801839	0.82[CEU][hapmap]
rs3801853	0.92[JPT][hapmap]
rs3801860	0.92[JPT][hapmap]
rs3801864	0.92[JPT][hapmap]
rs471536	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722631	0.91[JPT][hapmap]
rs475238	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476098	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484426	0.80[EUR][1000 genomes]
rs5012512	0.91[JPT][hapmap]
rs503110	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs504955	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532320	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534981	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556402	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564260	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567124	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57027817	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs580904	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs601106	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs607099	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622011	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639221	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640512	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643036	0.81[EUR][1000 genomes]
rs6461961	0.92[JPT][hapmap]
rs6461964	0.83[JPT][hapmap]
rs6461965	0.92[JPT][hapmap]
rs6461971	0.92[JPT][hapmap]
rs667841	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs687603	0.81[EUR][1000 genomes]
rs688039	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970591	0.92[JPT][hapmap]
rs6973237	0.92[JPT][hapmap]
rs774367	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784206	0.80[AMR][1000 genomes]
rs7799888	0.82[JPT][hapmap]
rs7807640	0.91[JPT][hapmap]
rs7810109	0.83[JPT][hapmap]
rs7810127	0.83[JPT][hapmap]
rs891876	0.91[JPT][hapmap]
rs9648020	0.92[JPT][hapmap]
rs989250	0.92[JPT][hapmap]

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	nsv887855	chr7:26823963-26872652	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2769365	HOTAIRM1	cis	Whole Blood	GTEx
rs2769365	SKAP2	cis	Whole Blood	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26808000-26854800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:26812400-26849000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:26813000-26871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:26823000-26846400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:26836600-26846200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr7:26839400-26871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:26843200-26851800	Weak transcription	Fetal Lung	lung
9	chr7:26843400-26846200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:26843400-26846200	Weak transcription	Primary B cells from cord blood	blood
11	chr7:26843600-26870800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:26843600-26871400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:26843800-26863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:26844000-26846600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:26844200-26849600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr7:26844400-26853200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:26844600-26846600	Weak transcription	Ovary	ovary

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