Variant report

Variant	rs6588566
Chromosome Location	chr1:56048120-56048121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10493196	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10749702	0.86[EUR][1000 genomes]
rs11206625	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11206629	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11206636	0.86[EUR][1000 genomes]
rs11206637	0.86[EUR][1000 genomes]
rs11206639	0.86[EUR][1000 genomes]
rs11807964	0.82[AMR][1000 genomes]
rs12026971	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12040862	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12086546	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12128337	0.81[EUR][1000 genomes]
rs12132336	0.86[EUR][1000 genomes]
rs12139752	0.86[EUR][1000 genomes]
rs12142554	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12401977	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1392128	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1392129	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1392130	0.86[EUR][1000 genomes]
rs1392131	0.85[EUR][1000 genomes]
rs1392132	0.86[EUR][1000 genomes]
rs1587432	0.86[EUR][1000 genomes]
rs17112402	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61774741	0.82[AMR][1000 genomes]
rs61776360	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6669248	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6675850	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7525515	0.86[EUR][1000 genomes]
rs7556008	0.86[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	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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56040600-56058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:56042200-56049600	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:56042200-56052400	Weak transcription	Right Atrium	heart
4	chr1:56043000-56049600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:56043000-56049800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:56043000-56050200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:56043000-56050400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:56044400-56051400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:56044600-56048400	Enhancers	HSMM	muscle
10	chr1:56045000-56048200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:56045000-56048400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:56045200-56048200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:56045200-56048400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:56045200-56050000	Weak transcription	Ovary	ovary
15	chr1:56045400-56048600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:56045600-56049600	Weak transcription	Fetal Stomach	stomach
17	chr1:56045800-56048400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:56046000-56048200	Enhancers	NHLF	lung
19	chr1:56046000-56048400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:56046400-56048200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:56046600-56048600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:56047000-56048200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:56047000-56048400	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:56047000-56048400	Enhancers	HMEC	breast
25	chr1:56047000-56048600	Enhancers	NHDF-Ad	bronchial
26	chr1:56047000-56049600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:56047000-56049600	Weak transcription	Fetal Lung	lung
28	chr1:56047000-56050000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:56047000-56050000	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:56047000-56050000	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:56047000-56050200	Weak transcription	Brain Anterior Caudate	brain
32	chr1:56047000-56050400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:56047000-56050400	Weak transcription	Brain Substantia Nigra	brain
34	chr1:56047000-56050400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:56047000-56050400	Weak transcription	Hela-S3	cervix
36	chr1:56047000-56051400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:56047200-56048200	Enhancers	Aorta	Aorta
38	chr1:56047200-56048200	Enhancers	Psoas Muscle	Psoas
39	chr1:56047200-56048400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:56047200-56049000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:56047400-56048600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:56047400-56050400	Weak transcription	NH-A	brain
43	chr1:56047600-56050200	Weak transcription	Osteobl	bone
44	chr1:56048000-56049800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:56048000-56050400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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