Variant report

Variant	rs11169805
Chromosome Location	chr12:51725636-51725637
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	chr12:51715738..51718672-chr12:51724028..51726868,2	MCF-7	breast:
2	chr12:51724277..51726294-chr12:51726344..51728218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110934	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10516	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs10876162	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169795	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs11616158	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12310910	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12582273	1.00[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12829179	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12830766	0.86[AMR][1000 genomes]
rs12831721	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17860300	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17860301	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17860343	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3858624	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3858627	0.84[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs57941347	0.86[AMR][1000 genomes]
rs61022955	0.86[AMR][1000 genomes]
rs68042460	0.86[AMR][1000 genomes]
rs7133606	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7138439	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7299306	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7299453	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7306746	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7959814	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7964134	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9651999	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11169805	ELA1	cis	multi-tissue	Pritchard
rs11169805	LOC57228	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51718400-51727800	Weak transcription	Colonic Mucosa	Colon
2	chr12:51720800-51728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:51720800-51735000	Weak transcription	Esophagus	oesophagus
4	chr12:51721200-51735000	Weak transcription	NHDF-Ad	bronchial
5	chr12:51722600-51735000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:51724200-51726000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr12:51724200-51726200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:51724200-51727200	Weak transcription	K562	blood
9	chr12:51724200-51735000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:51724400-51727600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:51724400-51727600	Weak transcription	Hela-S3	cervix
12	chr12:51724400-51727800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:51724400-51728400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:51724400-51728600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:51724400-51728600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:51724400-51728600	Weak transcription	Fetal Thymus	thymus
17	chr12:51724400-51728800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:51724400-51728800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:51724400-51734800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:51724400-51739200	Weak transcription	Thymus	Thymus
21	chr12:51724600-51727800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:51724600-51728400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr12:51725000-51725800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr12:51725000-51725800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:51725000-51726000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr12:51725400-51735000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:51725600-51725800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr12:51725600-51726000	Enhancers	Rectal Mucosa Donor 31	rectum

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