Variant report

Variant	rs12401977
Chromosome Location	chr1:56042544-56042545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10493196	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10789002	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10789003	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10789004	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10888931	0.82[ASN][1000 genomes]
rs10888933	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10888934	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11206618	0.85[ASN][1000 genomes]
rs11206620	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11206622	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11206625	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11206629	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11206638	0.83[EUR][1000 genomes]
rs11807964	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12026971	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12040862	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12041985	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs12044949	0.82[ASN][1000 genomes]
rs12069408	0.81[ASN][1000 genomes]
rs12086546	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128185	0.85[ASN][1000 genomes]
rs12128337	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12142554	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1392128	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1392129	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1499658	0.85[ASN][1000 genomes]
rs1604016	0.83[EUR][1000 genomes]
rs17112402	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17417716	0.83[EUR][1000 genomes]
rs1875068	0.85[ASN][1000 genomes]
rs4339898	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4927249	0.83[ASN][1000 genomes]
rs56169646	0.83[EUR][1000 genomes]
rs61774741	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61776360	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61776375	0.83[EUR][1000 genomes]
rs61776377	0.83[EUR][1000 genomes]
rs6588566	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6669248	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6675850	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72667832	0.85[ASN][1000 genomes]
rs72667838	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72667846	0.86[ASN][1000 genomes]
rs7513395	0.83[EUR][1000 genomes]
rs7544458	0.83[EUR][1000 genomes]
rs7546899	0.83[EUR][1000 genomes]
rs7555929	0.83[EUR][1000 genomes]
rs904602	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs9436973	0.85[ASN][1000 genomes]
rs9787362	0.86[EUR][1000 genomes];0.87[ASN][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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56035400-56043200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:56037200-56047200	Weak transcription	Esophagus	oesophagus
3	chr1:56039000-56045200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:56039000-56045800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:56039000-56046000	Weak transcription	NHLF	lung
6	chr1:56039000-56046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:56039200-56045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:56039200-56047200	Weak transcription	Psoas Muscle	Psoas
9	chr1:56039400-56045000	Weak transcription	HSMMtube	muscle
10	chr1:56039600-56043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:56039600-56046200	Weak transcription	NH-A	brain
12	chr1:56040600-56058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:56041600-56044400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:56041800-56045000	Weak transcription	Osteobl	bone
15	chr1:56041800-56045200	Weak transcription	NHDF-Ad	bronchial
16	chr1:56042000-56042800	Weak transcription	Brain Germinal Matrix	brain
17	chr1:56042000-56043000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:56042000-56043000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:56042000-56043400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:56042000-56043800	Weak transcription	Right Ventricle	heart
21	chr1:56042000-56044000	Weak transcription	Fetal Lung	lung
22	chr1:56042000-56044600	Weak transcription	HSMM	muscle
23	chr1:56042000-56045000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:56042000-56046200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:56042000-56046400	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:56042000-56046600	Weak transcription	Brain Anterior Caudate	brain
27	chr1:56042000-56047400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:56042200-56044600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:56042200-56044600	Weak transcription	Left Ventricle	heart
30	chr1:56042200-56044600	Weak transcription	Lung	lung
31	chr1:56042200-56045000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:56042200-56046200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:56042200-56046200	Weak transcription	Brain Substantia Nigra	brain
34	chr1:56042200-56046400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:56042200-56046400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:56042200-56046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:56042200-56046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:56042200-56046600	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:56042200-56049600	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:56042200-56052400	Weak transcription	Right Atrium	heart

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