Variant report

Variant	rs9645752
Chromosome Location	chr12:12544266-12544267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1019340	0.81[CHB][hapmap]
rs10459098	0.80[CHB][hapmap]
rs10505765	0.83[JPT][hapmap]
rs10743982	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs10743983	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10743984	0.82[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap]
rs10772566	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs10772567	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10845530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845534	0.85[GIH][hapmap];0.80[MEX][hapmap]
rs10845539	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs10845544	0.80[JPT][hapmap]
rs10845545	0.81[CHB][hapmap]
rs12301872	0.80[MEX][hapmap]
rs16907990	0.88[JPT][hapmap]
rs16908059	0.83[JPT][hapmap]
rs16908062	0.83[JPT][hapmap]
rs16908072	0.83[JPT][hapmap]
rs16908076	0.83[JPT][hapmap]
rs16908101	0.83[JPT][hapmap]
rs2160586	0.81[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs2216264	0.80[CHB][hapmap]
rs3925170	0.81[CHB][hapmap]
rs4763825	0.81[CHB][hapmap]
rs4763829	0.81[CHB][hapmap]
rs7295080	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs73061463	0.83[ASN][1000 genomes]
rs7309503	0.81[CHB][hapmap]
rs7310012	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs7311363	0.84[ASN][1000 genomes]
rs7311364	0.81[CHB][hapmap]
rs7953025	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs7967111	0.81[CHB][hapmap]
rs7967230	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs7967466	0.80[CHB][hapmap]
rs7969849	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs888200	0.85[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1045637	chr12:12506839-12546747	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	esv2760275	chr12:12530073-12546759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv437141	chr12:12530718-12544266	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv818895	chr12:12532984-12544266	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv517152	chr12:12532984-12547645	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1041842	chr12:12536207-12546747	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9645752	ETV6	cis	cerebellum	SCAN
rs9645752	LOH12CR1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:12512000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:12519200-12549800	Weak transcription	Aorta	Aorta
4	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:12525400-12550200	Weak transcription	Fetal Stomach	stomach
6	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
8	chr12:12533000-12545800	Weak transcription	Pancreas	Pancrea
9	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:12533600-12555400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:12538200-12551000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:12538400-12545800	Weak transcription	Left Ventricle	heart
15	chr12:12538400-12548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:12538400-12549200	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:12538400-12550200	Weak transcription	Primary T cells from cord blood	blood
18	chr12:12538400-12551600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:12538400-12552800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:12538400-12555400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:12538400-12556200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:12538800-12551400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:12539400-12546800	Weak transcription	Stomach Mucosa	stomach
25	chr12:12539600-12545200	Weak transcription	Fetal Intestine Small	intestine
26	chr12:12539800-12545800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:12540200-12545000	Weak transcription	HepG2	liver
28	chr12:12540200-12545200	Weak transcription	Fetal Intestine Large	intestine
29	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:12540600-12549400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:12540600-12556200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:12540800-12550800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:12540800-12551000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:12540800-12553800	Weak transcription	GM12878-XiMat	blood
35	chr12:12540800-12555400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:12541000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:12541000-12545000	Weak transcription	Fetal Lung	lung
38	chr12:12541000-12545200	Weak transcription	Fetal Heart	heart
39	chr12:12541000-12550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:12541000-12550200	Weak transcription	Hela-S3	cervix
41	chr12:12541000-12550600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:12541000-12551000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:12541000-12551000	Weak transcription	Small Intestine	intestine
44	chr12:12541200-12545200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:12541200-12547000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:12541200-12549200	Weak transcription	NHLF	lung
47	chr12:12541400-12544400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:12541400-12547000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:12541400-12549200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:12541400-12550000	Weak transcription	NHDF-Ad	bronchial

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