Variant report

Variant	rs17466486
Chromosome Location	chr12:40722549-40722550
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	12:40716064-40722905..12:40793507-40812339	GM12878	blood:
2	chr12:40721972..40722829-chr4:110621913..110622453,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205592	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10506152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11175766	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs11175780	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11564129	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11564149	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11564150	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs11564180	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1388599	1.00[CHB][hapmap]
rs17444089	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17466080	1.00[CHB][hapmap]
rs17466178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs17466185	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17466521	0.80[ASN][1000 genomes]
rs17466626	1.00[CHB][hapmap]
rs17519881	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2046928	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2404834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41286474	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4423250	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7132073	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73102746	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7971935	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[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	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	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
2	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
3	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:40674400-40760400	Weak transcription	Lung	lung
5	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:40684000-40722600	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:40684000-40722600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:40684000-40725000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:40695800-40723600	Weak transcription	Brain Angular Gyrus	brain
11	chr12:40704400-40723800	Weak transcription	Brain Anterior Caudate	brain
12	chr12:40706800-40722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:40707800-40724400	Strong transcription	Primary B cells from cord blood	blood
14	chr12:40712000-40736600	Weak transcription	Left Ventricle	heart
15	chr12:40712000-40743400	Weak transcription	Aorta	Aorta
16	chr12:40714200-40759200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:40716800-40761600	Weak transcription	Fetal Kidney	kidney
18	chr12:40717800-40724600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:40719200-40723800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:40719600-40735200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:40720600-40723800	Weak transcription	A549	lung
22	chr12:40721000-40734000	Weak transcription	Esophagus	oesophagus
23	chr12:40721400-40722800	Strong transcription	Ovary	ovary
24	chr12:40721600-40723400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:40721600-40726000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr12:40721800-40722600	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:40721800-40723600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr12:40721800-40723800	Strong transcription	Adipose Nuclei	Adipose
29	chr12:40721800-40724800	Strong transcription	Liver	Liver
30	chr12:40722400-40722600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:40722400-40722600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:40722400-40723400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:40722400-40725600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:40722400-40726200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:40722400-40730800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:40722400-40736200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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