Variant report

Variant	rs17443552
Chromosome Location	chr12:40656677-40656678
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10506153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878244	1.00[ASN][1000 genomes]
rs10878246	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11564113	1.00[JPT][hapmap]
rs11564128	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564203	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564204	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613829	1.00[JPT][hapmap]
rs11829088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442346	1.00[JPT][hapmap]
rs17442353	1.00[JPT][hapmap]
rs17442490	1.00[JPT][hapmap]
rs17442882	1.00[JPT][hapmap]
rs17443421	1.00[JPT][hapmap]
rs17444096	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444103	1.00[JPT][hapmap]
rs17444542	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17444612	1.00[ASN][1000 genomes]
rs17458257	1.00[JPT][hapmap]
rs17458745	1.00[JPT][hapmap]
rs17458773	1.00[JPT][hapmap]
rs17458974	1.00[JPT][hapmap]
rs17465716	1.00[JPT][hapmap]
rs17465849	1.00[JPT][hapmap]
rs17465891	1.00[JPT][hapmap]
rs17465912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17466030	1.00[JPT][hapmap]
rs17466037	1.00[CHB][hapmap]
rs17466150	1.00[YRI][hapmap]
rs17466220	1.00[JPT][hapmap]
rs17466269	1.00[JPT][hapmap]
rs17466297	1.00[JPT][hapmap]
rs17466339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs17466430	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17466451	1.00[JPT][hapmap]
rs17466633	1.00[JPT][hapmap]
rs17467095	1.00[CHB][hapmap]
rs17483502	1.00[JPT][hapmap]
rs17489459	1.00[JPT][hapmap]
rs17489480	1.00[JPT][hapmap]
rs17489666	1.00[JPT][hapmap]
rs17490013	1.00[JPT][hapmap]
rs17490578	1.00[JPT][hapmap]
rs17490620	1.00[JPT][hapmap]
rs17490762	1.00[JPT][hapmap]
rs17491061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17491110	1.00[JPT][hapmap]
rs17491410	1.00[JPT][hapmap]
rs17492082	1.00[ASN][1000 genomes]
rs17492138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17518427	1.00[JPT][hapmap]
rs17518441	1.00[JPT][hapmap]
rs17518476	1.00[JPT][hapmap]
rs17518672	1.00[JPT][hapmap]
rs17518735	1.00[JPT][hapmap]
rs17519573	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17519797	1.00[JPT][hapmap]
rs17520251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17520278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17520634	1.00[JPT][hapmap]
rs17520655	1.00[JPT][hapmap]
rs1907632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114567	1.00[ASN][1000 genomes]
rs2244534	1.00[CHB][hapmap]
rs28365202	1.00[JPT][hapmap]
rs28365243	1.00[JPT][hapmap]
rs57997594	1.00[ASN][1000 genomes]
rs60776971	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61007767	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73275761	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73279554	1.00[ASN][1000 genomes]
rs73279557	1.00[ASN][1000 genomes]
rs9705735	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40619600-40661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:40619600-40678400	Weak transcription	Right Ventricle	heart
3	chr12:40619800-40658800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:40620800-40659200	Weak transcription	Brain Anterior Caudate	brain
5	chr12:40620800-40704200	Weak transcription	Esophagus	oesophagus
6	chr12:40621000-40659800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:40621000-40661200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:40622800-40661000	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:40622800-40708800	Weak transcription	Left Ventricle	heart
10	chr12:40630600-40669400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:40630600-40686400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:40640200-40680400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
14	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
15	chr12:40641200-40662800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:40642200-40682400	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:40643000-40659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:40646800-40658000	Weak transcription	A549	lung
19	chr12:40647600-40674000	Weak transcription	Lung	lung
20	chr12:40648600-40657600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:40648800-40659200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:40648800-40659800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:40649000-40659200	Weak transcription	Ovary	ovary
24	chr12:40649600-40657800	Weak transcription	Adipose Nuclei	Adipose
25	chr12:40649600-40659200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:40654200-40659000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:40654400-40659200	Weak transcription	Aorta	Aorta
28	chr12:40654600-40659000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:40654800-40659200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:40655200-40657200	Genic enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:40655200-40658400	Enhancers	Primary B cells from peripheral blood	blood
32	chr12:40655600-40658200	Enhancers	Primary B cells from cord blood	blood
33	chr12:40656000-40656800	Genic enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:40656000-40657200	Weak transcription	Liver	Liver
35	chr12:40656400-40659000	Weak transcription	Psoas Muscle	Psoas
36	chr12:40656600-40658000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:40656600-40658400	Enhancers	GM12878-XiMat	blood

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