Variant report

Variant	rs12526141
Chromosome Location	chr6:107030672-107030673
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	chr6:107028799..107031451-chr6:107035031..107036898,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1026622	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11759221	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11968064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12210786	0.99[EUR][1000 genomes]
rs12214557	0.99[EUR][1000 genomes]
rs12523774	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs13319	0.89[YRI][hapmap]
rs1419054	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs17052211	0.90[AFR][1000 genomes]
rs17052215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2066202	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs2126395	0.90[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs2219667	0.90[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2883075	0.94[EUR][1000 genomes]
rs3747790	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4945758	0.93[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4946763	0.94[ASN][1000 genomes]
rs4946768	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4946774	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs57332679	0.90[AFR][1000 genomes]
rs57424436	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58972320	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909966	0.80[AFR][1000 genomes]
rs6910512	0.81[AFR][1000 genomes]
rs6911512	0.98[EUR][1000 genomes]
rs7738230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7751749	0.99[EUR][1000 genomes]
rs7756852	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs8013	0.86[ASW][hapmap];0.89[YRI][hapmap]
rs9320182	0.86[ASW][hapmap];0.89[YRI][hapmap]
rs9384622	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9384623	0.99[EUR][1000 genomes]
rs9384624	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9386567	0.97[ASN][1000 genomes]
rs9386571	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs9386574	0.98[EUR][1000 genomes]
rs9398095	0.91[ASN][1000 genomes]
rs9400031	0.99[EUR][1000 genomes]
rs9400032	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9480685	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs9480687	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9480692	0.99[EUR][1000 genomes]
rs9486398	0.88[YRI][hapmap]
rs9486400	0.86[ASW][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs9486403	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9486404	0.86[ASW][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs9486406	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9486410	0.86[ASW][hapmap];0.89[YRI][hapmap]
rs9486411	0.86[ASW][hapmap];0.89[YRI][hapmap]
rs9486414	0.81[GIH][hapmap]
rs962476	1.00[CEU][hapmap];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12526141	SCML4	cis	parietal	SCAN
rs12526141	QRSL1	cis	parietal	SCAN
rs12526141	QRSL1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
3	chr6:107010200-107064600	Weak transcription	A549	lung
4	chr6:107014400-107038800	Weak transcription	Fetal Brain Female	brain
5	chr6:107016200-107039400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:107017000-107032800	Weak transcription	K562	blood
7	chr6:107017800-107041000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:107018000-107030800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:107018000-107052600	Weak transcription	Colonic Mucosa	Colon
10	chr6:107018400-107066400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:107018400-107076400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:107018600-107039000	Weak transcription	Placenta	Placenta
13	chr6:107018800-107039400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:107018800-107076200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:107019000-107076200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:107019200-107034800	Weak transcription	GM12878-XiMat	blood
17	chr6:107019400-107034400	Weak transcription	NHEK	skin
18	chr6:107019400-107035200	Weak transcription	Fetal Lung	lung
19	chr6:107019800-107076400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:107020200-107037600	Weak transcription	Fetal Heart	heart
21	chr6:107020600-107032200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr6:107021600-107033400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:107022000-107076400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:107023000-107030800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:107023200-107038200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr6:107023200-107038600	Weak transcription	Brain Germinal Matrix	brain
27	chr6:107023400-107030800	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:107023400-107030800	Weak transcription	Lung	lung
29	chr6:107023400-107033200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:107023400-107034200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:107023400-107034200	Weak transcription	Right Ventricle	heart
32	chr6:107023400-107034400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:107023400-107034600	Weak transcription	Hela-S3	cervix
34	chr6:107023400-107038200	Weak transcription	HSMM	muscle
35	chr6:107023400-107038600	Weak transcription	NH-A	brain
36	chr6:107023400-107039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:107023400-107039600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:107023400-107050200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:107023400-107068800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:107023400-107076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:107023600-107032000	Weak transcription	Aorta	Aorta
42	chr6:107023600-107038800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:107023800-107034600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:107024200-107035200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:107024600-107030800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:107024600-107030800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:107026200-107035000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:107026400-107038800	Weak transcription	Brain Anterior Caudate	brain
49	chr6:107027600-107030800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:107027600-107038600	Weak transcription	NHDF-Ad	bronchial

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