Variant report

Variant	rs12640186
Chromosome Location	chr4:3374539-3374540
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	chr4:3372648..3375101-chr4:3385736..3387279,2	K562	blood:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12640526	0.94[ASN][1000 genomes]
rs12640721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12643903	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16844197	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16844201	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073286	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs2281470	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2343799	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2749775	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2749776	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2749779	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749786	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857859	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2857860	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3129329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3129330	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3129331	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3129332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129333	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129336	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58949283	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62274923	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62274924	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73193371	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73193372	0.98[ASN][1000 genomes]
rs881818	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12640186	RGS12	cis	cerebellum	SCAN
rs12640186	WHSC2	cis	cerebellum	SCAN
rs12640186	DOK7	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3368800-3376800	Enhancers	Spleen	Spleen
2	chr4:3369200-3374800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:3370400-3374600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:3371200-3375800	Weak transcription	Gastric	stomach
5	chr4:3371600-3378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:3371800-3376000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:3372000-3375000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:3372200-3375600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr4:3372200-3375600	Enhancers	Adipose Nuclei	Adipose
10	chr4:3372200-3377400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:3372200-3377600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:3372200-3378000	Weak transcription	Aorta	Aorta
13	chr4:3372200-3382000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:3372200-3386400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:3372400-3374600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:3372400-3375000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:3372400-3375000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:3372400-3375000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:3372400-3375200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:3372400-3375200	Enhancers	Left Ventricle	heart
21	chr4:3372400-3375400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr4:3372400-3375400	Enhancers	Right Ventricle	heart
23	chr4:3372400-3375600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr4:3372400-3375600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:3372400-3377400	Weak transcription	Osteobl	bone
26	chr4:3372400-3377800	Weak transcription	NHDF-Ad	bronchial
27	chr4:3372400-3382000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:3372600-3374600	Enhancers	Right Atrium	heart
29	chr4:3372600-3377400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:3372600-3377600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:3372800-3375200	Enhancers	Ovary	ovary
32	chr4:3373000-3374800	Weak transcription	Esophagus	oesophagus
33	chr4:3373000-3375000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:3373000-3376200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:3373000-3378000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:3373000-3389000	Weak transcription	Psoas Muscle	Psoas
37	chr4:3373200-3374600	Weak transcription	NHLF	lung
38	chr4:3373200-3374800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:3373200-3375600	Enhancers	Fetal Thymus	thymus
40	chr4:3373400-3375000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:3373400-3375400	Enhancers	Placenta	Placenta
42	chr4:3373400-3375600	Enhancers	Lung	lung
43	chr4:3373400-3375800	Enhancers	Primary B cells from peripheral blood	blood
44	chr4:3373400-3377400	Weak transcription	HepG2	liver
45	chr4:3373400-3377600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:3373400-3377600	Weak transcription	HSMMtube	muscle
47	chr4:3373400-3380800	Weak transcription	Brain Angular Gyrus	brain
48	chr4:3373400-3382000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:3373400-3388400	Weak transcription	Fetal Kidney	kidney
50	chr4:3373400-3388800	Weak transcription	Colon Smooth Muscle	Colon

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