Variant report

Variant	rs13085477
Chromosome Location	chr3:28300347-28300348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10510606	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11129312	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11129313	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11129314	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129317	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11708368	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11708635	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717202	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11921526	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12106806	0.84[EUR][1000 genomes]
rs12107556	0.84[EUR][1000 genomes]
rs12485853	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12485858	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12497510	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069450	0.84[EUR][1000 genomes]
rs13069777	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13073936	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13074515	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13085236	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092179	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1606391	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34109684	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34692982	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35504778	0.95[EUR][1000 genomes]
rs35813951	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680746	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6782956	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785465	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792110	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792215	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6798266	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7624015	0.83[EUR][1000 genomes]
rs7624111	0.83[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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28283800-28311400	Weak transcription	Lung	lung
2	chr3:28284000-28304800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:28284000-28309600	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:28284000-28313800	Weak transcription	Ovary	ovary
5	chr3:28284000-28317200	Weak transcription	Gastric	stomach
6	chr3:28284400-28305400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:28284400-28305800	Weak transcription	Hela-S3	cervix
8	chr3:28284400-28311000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:28284400-28312600	Weak transcription	Fetal Lung	lung
10	chr3:28284400-28321800	Weak transcription	NHLF	lung
11	chr3:28284600-28305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:28284600-28306000	Weak transcription	A549	lung
13	chr3:28284600-28307200	Weak transcription	Fetal Intestine Large	intestine
14	chr3:28284600-28311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:28285200-28305200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:28285200-28305600	Weak transcription	Fetal Thymus	thymus
17	chr3:28285600-28315400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:28285800-28305400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:28285800-28311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:28286000-28306000	Weak transcription	K562	blood
21	chr3:28286000-28307200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:28287200-28304800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:28287600-28317000	Weak transcription	Pancreas	Pancrea
24	chr3:28288600-28305200	Weak transcription	Liver	Liver
25	chr3:28288600-28311200	Weak transcription	Esophagus	oesophagus
26	chr3:28289400-28305200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:28289400-28305200	Weak transcription	Dnd41	blood
28	chr3:28291400-28311200	Weak transcription	Aorta	Aorta
29	chr3:28292200-28305800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:28292800-28300800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:28292800-28311000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:28293000-28305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:28293000-28305600	Weak transcription	Left Ventricle	heart
34	chr3:28293200-28305600	Weak transcription	Primary T cells from cord blood	blood
35	chr3:28293600-28305600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:28293600-28311200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:28293800-28305800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:28293800-28309800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:28294000-28309200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:28294200-28314400	Weak transcription	HepG2	liver
41	chr3:28294400-28313800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:28294400-28314200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:28294600-28304200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:28294600-28313800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:28294800-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:28294800-28305200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:28294800-28313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:28294800-28316400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:28295000-28303000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:28295000-28305200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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