Variant report

Variant	rs13213488
Chromosome Location	chr6:39498554-39498555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10484823	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11751847	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752175	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752438	0.82[ASN][1000 genomes]
rs11754807	0.82[ASN][1000 genomes]
rs11754808	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755434	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757080	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759743	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525519	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528130	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200342	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209820	0.94[EUR][1000 genomes]
rs13213322	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536700	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892194	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34081723	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34720944	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35516457	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4714258	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4714261	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55749620	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56713174	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56951565	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6458119	0.94[EUR][1000 genomes]
rs6901155	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6905995	0.94[EUR][1000 genomes]
rs6913556	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6927837	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928195	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928537	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942056	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571377	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732127	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73732138	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73732153	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7751353	0.95[EUR][1000 genomes]
rs7751706	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7751942	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754249	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771470	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774528	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296301	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9380876	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9471123	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9471124	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9471129	0.82[AMR][1000 genomes];0.94[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	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv885823	chr6:39421715-39526867	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39488600-39509400	Weak transcription	Brain Substantia Nigra	brain
2	chr6:39495200-39511000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:39497800-39498600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr6:39497800-39498600	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:39497800-39498600	Active TSS	Aorta	Aorta
6	chr6:39497800-39498600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr6:39497800-39498600	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr6:39498000-39498600	Enhancers	Brain Cingulate Gyrus	brain
9	chr6:39498000-39498600	Active TSS	Colon Smooth Muscle	Colon
10	chr6:39498000-39499200	Enhancers	Duodenum Mucosa	Duodenum
11	chr6:39498200-39498600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:39498200-39498600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr6:39498200-39498600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:39498200-39498600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:39498200-39498600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:39498200-39498600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr6:39498200-39498600	Active TSS	Brain Anterior Caudate	brain
18	chr6:39498200-39498600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr6:39498200-39498600	Enhancers	Fetal Stomach	stomach
20	chr6:39498200-39498600	Active TSS	Ovary	ovary
21	chr6:39498200-39498600	Active TSS	Rectal Smooth Muscle	rectum
22	chr6:39498200-39498600	Active TSS	GM12878-XiMat	blood
23	chr6:39498200-39498600	Flanking Active TSS	NH-A	brain
24	chr6:39498200-39498600	Flanking Active TSS	NHDF-Ad	bronchial
25	chr6:39498400-39498600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:39498400-39498600	Enhancers	HMEC	breast
27	chr6:39498400-39498600	Active TSS	Osteobl	bone
28	chr6:39498400-39498800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:39498400-39499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:39498400-39509400	Weak transcription	Brain Hippocampus Middle	brain

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