Variant report

Variant	rs11926145
Chromosome Location	chr3:151019928-151019929
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151017110..151019943-chr3:151020802..151024030,3	MCF-7	breast:
2	chr3:151011307..151016157-chr3:151019117..151025599,7	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10513391	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935831	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935832	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935833	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10935839	0.87[CEU][hapmap]
rs11925037	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12107539	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12485537	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12486265	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12497019	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497330	0.87[CEU][hapmap]
rs12636396	0.94[CHB][hapmap]
rs12637988	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12639390	0.82[CHB][hapmap]
rs13079391	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095610	0.87[CEU][hapmap]
rs1388617	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16863287	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1882013	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap]
rs2307020	0.87[CEU][hapmap]
rs28527299	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34347156	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34708786	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35144003	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35786948	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732759	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs3773621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806636	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680256	0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap]
rs4680263	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs4680307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680315	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680356	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55705054	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56087525	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62282988	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62283022	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440738	0.87[CEU][hapmap]
rs66524723	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66927386	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767192	0.87[CEU][hapmap]
rs6784934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6785930	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6790448	0.87[CEU][hapmap]
rs6793898	0.86[CEU][hapmap]
rs6796501	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6801155	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6801273	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs6804769	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs6808091	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7428575	0.87[CEU][hapmap]
rs7618206	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7644001	0.87[CEU][hapmap];0.80[TSI][hapmap]
rs7648875	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11926145	MED12L	cis	cerebellum	SCAN
rs11926145	CLRN1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:151010200-151022200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:151011400-151021800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:151011800-151021600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:151012400-151021600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:151012800-151021600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:151014400-151021800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:151014400-151022400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:151014400-151022600	Weak transcription	Esophagus	oesophagus
11	chr3:151015200-151021800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:151017000-151021600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:151017000-151022600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:151018000-151020000	Enhancers	NHLF	lung
15	chr3:151018200-151021600	Genic enhancers	HMEC	breast
16	chr3:151018200-151022000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:151019000-151020200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:151019000-151020800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:151019000-151022400	Genic enhancers	NHEK	skin
20	chr3:151019200-151020200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:151019200-151020200	Enhancers	Osteobl	bone
22	chr3:151019200-151021000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:151019400-151020200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:151019400-151020200	Enhancers	NH-A	brain
25	chr3:151019400-151020200	Enhancers	NHDF-Ad	bronchial
26	chr3:151019400-151020600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:151019400-151020600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:151019400-151020600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:151019400-151020800	Enhancers	Hela-S3	cervix

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