Variant report

Variant	rs1179947
Chromosome Location	chr12:122442444-122442445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122440790..122443569-chr12:122445704..122448468,2	MCF-7	breast:
2	chr12:122440832..122442485-chr12:122443851..122445815,2	K562	blood:
3	chr12:122237113..122238694-chr12:122441857..122444463,2	K562	blood:
4	chr12:122441336..122445469-chr12:122458589..122461636,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139725	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1169076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1169081	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1169083	0.99[ASN][1000 genomes]
rs1169084	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1169086	0.99[ASN][1000 genomes]
rs1169087	0.98[ASN][1000 genomes]
rs1169091	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1177588	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1184893	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12578258	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12579389	0.80[ASN][1000 genomes]
rs1375653	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1375654	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1375655	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1630699	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1667586	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678952	0.85[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678953	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678970	0.88[ASN][1000 genomes]
rs1720030	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1720035	0.88[TSI][hapmap]
rs1720068	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs17852561	0.81[ASN][1000 genomes]
rs1814592	0.98[ASN][1000 genomes]
rs2009257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2018749	0.85[ASN][1000 genomes]
rs2272133	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2272135	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2309275	0.87[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2688411	0.80[EUR][1000 genomes]
rs2948663	0.80[EUR][1000 genomes]
rs55929316	0.86[ASN][1000 genomes]
rs59972569	0.80[ASN][1000 genomes]
rs686220	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7313748	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs745327	0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs830115	0.88[ASN][1000 genomes]
rs830120	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs830121	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs895960	0.88[TSI][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1179947	MSI1	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122422800-122442600	Weak transcription	Fetal Kidney	kidney
2	chr12:122438000-122444400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:122438600-122443600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:122439400-122443200	Enhancers	Brain Substantia Nigra	brain
5	chr12:122439800-122445200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:122440400-122443400	Enhancers	Brain Angular Gyrus	brain
7	chr12:122440400-122445800	Enhancers	Primary hematopoietic stem cells	blood
8	chr12:122440600-122442600	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:122440600-122443000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr12:122440600-122443400	Enhancers	Brain Hippocampus Middle	brain
11	chr12:122440800-122443400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:122440800-122445000	Weak transcription	Brain Germinal Matrix	brain
13	chr12:122441000-122442600	Enhancers	Primary B cells from cord blood	blood
14	chr12:122441000-122443400	Enhancers	Fetal Stomach	stomach
15	chr12:122441000-122445600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:122441200-122442600	Weak transcription	Brain Anterior Caudate	brain
17	chr12:122441200-122443000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:122441400-122442600	Enhancers	NH-A	brain
19	chr12:122441400-122443000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:122441400-122443000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:122441400-122443200	Enhancers	NHLF	lung
22	chr12:122441600-122443000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:122441600-122443000	Enhancers	NHDF-Ad	bronchial
24	chr12:122441600-122443400	Enhancers	Fetal Heart	heart
25	chr12:122441600-122443400	Enhancers	Fetal Muscle Leg	muscle
26	chr12:122441600-122443600	Enhancers	Spleen	Spleen
27	chr12:122441600-122443600	Flanking Active TSS	Dnd41	blood
28	chr12:122441600-122444000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:122441600-122444200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:122441600-122444800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:122441600-122444800	Flanking Active TSS	Fetal Thymus	thymus
32	chr12:122441600-122445800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:122441800-122442800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:122441800-122442800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:122441800-122443000	Enhancers	Lung	lung
36	chr12:122441800-122443400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:122441800-122443400	Enhancers	Left Ventricle	heart
38	chr12:122441800-122443600	Flanking Active TSS	Thymus	Thymus
39	chr12:122441800-122444200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr12:122441800-122444200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:122441800-122444200	Enhancers	GM12878-XiMat	blood
42	chr12:122441800-122444400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr12:122441800-122444400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr12:122441800-122445800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:122441800-122445800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr12:122442000-122442600	Enhancers	Aorta	Aorta
47	chr12:122442000-122442800	Enhancers	Right Atrium	heart
48	chr12:122442000-122443000	Enhancers	Adipose Nuclei	Adipose
49	chr12:122442000-122443000	Enhancers	Fetal Lung	lung
50	chr12:122442000-122443000	Flanking Active TSS	HSMM	muscle

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