Variant report

Variant	rs12526194
Chromosome Location	chr6:53809024-53809025
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	chr6:53805147..53806830-chr6:53806869..53810156,3	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1076701	1.00[CEU][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs1076702	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2073020	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2076495	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2294790	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2294791	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3777661	0.87[AMR][1000 genomes]
rs9349685	0.93[CEU][hapmap]
rs9357776	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9357778	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370233	0.94[CEU][hapmap];0.83[JPT][hapmap]
rs9370244	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9370246	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382243	0.94[CEU][hapmap]
rs9382252	0.82[AMR][1000 genomes]
rs9382254	0.94[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs9382256	0.84[AMR][1000 genomes]
rs9382257	0.95[EUR][1000 genomes]
rs9395878	0.94[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12526194	MRPS31	trans	cerebellum	SCAN
rs12526194	LRRC1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53787800-53810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:53794800-53815600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:53795600-53826200	Weak transcription	NHEK	skin
4	chr6:53799800-53810600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:53807200-53809800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:53807400-53809400	Enhancers	Brain Anterior Caudate	brain
7	chr6:53807400-53809400	Enhancers	Brain Cingulate Gyrus	brain
8	chr6:53807400-53810400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:53807600-53809400	Enhancers	Brain Substantia Nigra	brain
10	chr6:53807600-53809600	Enhancers	Brain Hippocampus Middle	brain
11	chr6:53807800-53809200	Enhancers	Aorta	Aorta
12	chr6:53807800-53809200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:53807800-53809400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:53807800-53809400	Enhancers	Fetal Lung	lung
15	chr6:53807800-53809600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr6:53807800-53810400	Weak transcription	Dnd41	blood
17	chr6:53808000-53809200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr6:53808000-53810200	Weak transcription	Fetal Thymus	thymus
19	chr6:53808000-53810400	Enhancers	Fetal Muscle Leg	muscle
20	chr6:53808400-53809600	Enhancers	Brain Germinal Matrix	brain
21	chr6:53808400-53811800	Weak transcription	Right Atrium	heart
22	chr6:53808600-53809200	Weak transcription	Ovary	ovary
23	chr6:53808600-53809400	Enhancers	Colon Smooth Muscle	Colon
24	chr6:53809000-53810200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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