Variant report

Variant	rs1388596
Chromosome Location	chr12:40640626-40640627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10506148	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10784528	0.86[CHB][hapmap]
rs10878123	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs11175256	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs11175401	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs11175422	0.84[JPT][hapmap]
rs11564115	0.90[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1388593	0.87[ASN][1000 genomes]
rs1472117	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1491924	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs1491939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491942	0.81[CHB][hapmap]
rs17484286	0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs1817817	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1907630	0.87[ASN][1000 genomes]
rs1907631	0.87[ASN][1000 genomes]
rs1907634	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2131088	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172240	0.87[ASN][1000 genomes]
rs2172241	0.87[ASN][1000 genomes]
rs2201144	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708426	0.87[ASN][1000 genomes]
rs2708436	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708437	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708438	0.87[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708441	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2723260	0.87[ASN][1000 genomes]
rs2723268	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2723269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4465428	0.86[CHB][hapmap]
rs4473003	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs4767971	0.86[CHB][hapmap]
rs7131694	0.86[CHB][hapmap]
rs7134572	0.95[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs715402	0.86[CHB][hapmap]
rs7307310	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs7963086	0.86[CHB][hapmap]
rs949640	0.80[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1045408	chr12:40620554-40664424	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
4	nsv1042967	chr12:40629636-40710319	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	esv3434685	chr12:40640535-40642683	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40619400-40644400	Weak transcription	Gastric	stomach
2	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
4	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:40620400-40644200	Weak transcription	Brain Angular Gyrus	brain
6	chr12:40620800-40644200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:40620800-40648000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:40620800-40659200	Weak transcription	Brain Anterior Caudate	brain
9	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
10	chr12:40621000-40643800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:40621000-40659800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:40621000-40661200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:40622800-40661000	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
15	chr12:40630600-40643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:40630600-40669400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:40630600-40686400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:40631200-40646600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:40632000-40655200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:40632000-40656000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr12:40633200-40643800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:40633400-40646600	Weak transcription	Ovary	ovary
23	chr12:40633400-40654200	Weak transcription	Aorta	Aorta
24	chr12:40635000-40647400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:40635000-40647400	Weak transcription	Lung	lung
26	chr12:40635200-40648200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:40636200-40648000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:40636200-40648200	Weak transcription	NHDF-Ad	bronchial
29	chr12:40636400-40643600	Weak transcription	Adipose Nuclei	Adipose
30	chr12:40637400-40640800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:40637400-40647200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:40638200-40641800	Weak transcription	Primary B cells from cord blood	blood
33	chr12:40639600-40643600	Weak transcription	Liver	Liver
34	chr12:40640200-40680400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:40640400-40640800	Enhancers	A549	lung
36	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
37	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea

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