Variant report

Variant	rs1274135
Chromosome Location	chr10:91686710-91686711
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	chr10:91685460..91687042-chr10:91688949..91691797,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10509584	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10785927	1.00[ASN][1000 genomes]
rs10785930	1.00[ASN][1000 genomes]
rs10881718	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1111716	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1113984	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11185944	1.00[ASN][1000 genomes]
rs12413697	1.00[CHB][hapmap]
rs1274129	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274131	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274132	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274137	1.00[ASN][1000 genomes]
rs1274139	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274140	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274141	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274142	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274172	1.00[ASN][1000 genomes]
rs1274174	1.00[ASN][1000 genomes]
rs1274177	1.00[ASN][1000 genomes]
rs1296513	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343365	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555825	1.00[ASN][1000 genomes]
rs1748492	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1748493	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1748495	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777944	0.81[EUR][1000 genomes]
rs1777945	0.81[EUR][1000 genomes]
rs1777954	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777955	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1954410	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026553	1.00[CHB][hapmap]
rs2419351	1.00[ASN][1000 genomes]
rs2763324	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2763331	0.89[EUR][1000 genomes]
rs2763332	0.84[EUR][1000 genomes]
rs2763333	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798613	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798616	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2798620	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272711	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4288675	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4301707	1.00[ASN][1000 genomes]
rs4933167	1.00[CHB][hapmap]
rs4933534	1.00[ASN][1000 genomes]
rs6583665	0.81[EUR][1000 genomes]
rs6583667	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6583671	1.00[ASN][1000 genomes]
rs67801980	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67876331	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092902	1.00[ASN][1000 genomes]
rs7094046	1.00[ASN][1000 genomes]
rs72820721	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72820722	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv949678	chr10:91589048-92016474	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv895883	chr10:91610601-92195828	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1039731	chr10:91645718-92198264	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv540743	chr10:91645718-92198264	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv467430	chr10:91681344-92297943	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv551875	chr10:91681344-92297943	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1274135	HOXB2	trans	lymphoblastoid	seeQTL
rs1274135	CYP26C1	cis	parietal	SCAN
rs1274135	ACTA2	cis	lymphoblastoid	seeQTL
rs1274135	IFIT1	cis	lymphoblastoid	seeQTL
rs1274135	IFIT3	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91684600-91686800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:91684600-91699600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:91686200-91687000	Strong transcription	Primary B cells from cord blood	blood
4	chr10:91686400-91687000	Enhancers	NHEK	skin
5	chr10:91686400-91687200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:91686400-91687200	Enhancers	HMEC	breast

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