Variant report

Variant	rs11609027
Chromosome Location	chr12:49801156-49801157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49783532..49785433-chr12:49799116..49801769,2	K562	blood:
2	chr12:49800023..49802561-chr12:49803485..49806694,3	K562	blood:
3	chr12:49800386..49802977-chr12:49804576..49806694,3	K562	blood:
4	chr12:49797720..49799411-chr12:49800332..49803280,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11608534	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11609068	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs11609087	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11609549	1.00[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs11609699	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11610501	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11610835	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11611624	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11611801	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11612426	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11613171	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11613183	0.82[EUR][1000 genomes]
rs11613509	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11613622	0.89[EUR][1000 genomes]
rs11613908	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11614120	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11614479	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11614854	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11615299	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11615316	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11615383	0.90[EUR][1000 genomes]
rs11829969	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11830595	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11830747	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11831792	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11834236	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11837194	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11838223	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12319484	0.83[EUR][1000 genomes]
rs2091801	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55712069	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56746050	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56784507	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58082501	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60827238	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61638922	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7296220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7296303	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7300276	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7301723	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7304456	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7309610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7488206	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7488270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49764000-49807400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:49764200-49804200	Weak transcription	Primary B cells from cord blood	blood
3	chr12:49764200-49840200	Weak transcription	Fetal Lung	lung
4	chr12:49764400-49822200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:49766600-49822200	Weak transcription	NH-A	brain
6	chr12:49768400-49819200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:49781600-49810000	Weak transcription	Right Ventricle	heart
8	chr12:49783200-49804200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:49783600-49816400	Weak transcription	Left Ventricle	heart
10	chr12:49784000-49804200	Weak transcription	GM12878-XiMat	blood
11	chr12:49784000-49806800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:49788000-49822600	Weak transcription	HUVEC	blood vessel
13	chr12:49791400-49819200	Weak transcription	Osteobl	bone
14	chr12:49791800-49817000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:49792800-49812600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:49792800-49819200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:49792800-49822000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:49793000-49818600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:49794400-49812400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:49795000-49806800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:49796000-49808200	Weak transcription	Lung	lung
22	chr12:49797000-49801600	Weak transcription	Gastric	stomach
23	chr12:49798000-49801400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:49798000-49807200	Weak transcription	HepG2	liver
25	chr12:49798000-49809000	Weak transcription	Dnd41	blood
26	chr12:49798000-49810600	Weak transcription	Fetal Intestine Large	intestine
27	chr12:49798000-49812800	Weak transcription	Fetal Intestine Small	intestine
28	chr12:49798000-49820800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:49798200-49802000	Weak transcription	Thymus	Thymus
30	chr12:49798400-49806000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:49798400-49806400	Weak transcription	HMEC	breast
32	chr12:49798400-49807400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:49798400-49856000	Weak transcription	Primary T cells from cord blood	blood
34	chr12:49798600-49804400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:49798600-49806600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:49798600-49811600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:49798600-49812400	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:49798600-49818400	Weak transcription	Fetal Stomach	stomach
39	chr12:49798600-49821800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:49798600-49822600	Weak transcription	Fetal Thymus	thymus
41	chr12:49798600-49840000	Weak transcription	Hela-S3	cervix
42	chr12:49799000-49806600	Weak transcription	NHDF-Ad	bronchial
43	chr12:49799400-49819000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr12:49799800-49802200	Weak transcription	Fetal Brain Male	brain
45	chr12:49800600-49801400	Strong transcription	A549	lung
46	chr12:49800600-49804400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:49800800-49801200	Strong transcription	NHEK	skin
48	chr12:49800800-49801400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:49801000-49801800	Strong transcription	Rectal Mucosa Donor 29	rectum

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