Variant report

Variant	rs12419342
Chromosome Location	chr11:47468545-47468546
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	chr11:47466850..47468725-chr11:47468990..47470844,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165917	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1044269	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10742805	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10742806	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742816	0.94[JPT][hapmap]
rs10769267	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11819955	0.94[JPT][hapmap]
rs11820650	0.82[ASN][1000 genomes]
rs11820680	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11821917	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11824864	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11828339	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12282783	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1474056	0.94[JPT][hapmap]
rs17198158	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs17790804	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2138767	0.94[JPT][hapmap]
rs2242511	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3740684	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740685	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781628	0.81[ASN][1000 genomes]
rs3824867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847503	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4147730	0.94[JPT][hapmap]
rs4237544	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4282946	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752783	0.94[JPT][hapmap]
rs4752786	0.94[JPT][hapmap]
rs4752829	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752836	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752839	0.89[JPT][hapmap]
rs4752843	0.94[JPT][hapmap]
rs4752992	0.81[ASN][1000 genomes]
rs60380053	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60882887	0.83[ASN][1000 genomes]
rs61000762	0.83[ASN][1000 genomes]
rs7101772	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7104366	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7105122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107853	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7108143	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7111873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7117277	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7119556	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7125468	0.83[ASN][1000 genomes]
rs7126210	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7130693	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753812	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7931089	0.93[JPT][hapmap]
rs7948705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9666924	0.94[JPT][hapmap]
rs9734013	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9919526	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[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	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Intraocular pressure	25173106	GWAS catalog

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47453400-47469200	Weak transcription	Psoas Muscle	Psoas
3	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
4	chr11:47456600-47468600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:47457400-47480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:47457400-47480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:47457400-47488400	Weak transcription	Gastric	stomach
8	chr11:47457800-47469000	Weak transcription	Spleen	Spleen
9	chr11:47459800-47469400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:47459800-47470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:47459800-47480600	Weak transcription	Fetal Intestine Small	intestine
12	chr11:47459800-47480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:47460000-47470800	Weak transcription	Lung	lung
14	chr11:47460000-47475600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:47460600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:47461800-47480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:47463600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:47463600-47469200	Weak transcription	Placenta	Placenta
19	chr11:47463600-47469400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:47464000-47481000	Weak transcription	NHEK	skin
21	chr11:47464800-47468600	Weak transcription	HSMMtube	muscle
22	chr11:47465000-47480800	Weak transcription	Adipose Nuclei	Adipose
23	chr11:47465200-47469000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:47465200-47475600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:47465400-47468600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:47465400-47470400	Weak transcription	Left Ventricle	heart
27	chr11:47465800-47480800	Weak transcription	Primary T cells from cord blood	blood
28	chr11:47466000-47471200	Weak transcription	Liver	Liver
29	chr11:47466000-47475600	Weak transcription	Fetal Thymus	thymus
30	chr11:47466200-47469000	Weak transcription	HepG2	liver
31	chr11:47467600-47469000	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr11:47467800-47468800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr11:47467800-47475600	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:47468000-47468800	Enhancers	HUVEC	blood vessel
35	chr11:47468200-47469000	Genic enhancers	Fetal Muscle Leg	muscle
36	chr11:47468400-47469600	Transcr. at gene 5' and 3'	HSMM	muscle

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