Variant report

Variant	rs13090296
Chromosome Location	chr3:28283736-28283737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:27809091..27811798-chr3:28283173..28285576,2	MCF-7	breast:
2	chr3:28282338..28284629-chr3:28303115..28305823,2	K562	blood:
3	chr3:28279814..28284603-chr3:28388127..28392296,9	K562	blood:
4	chr3:28283572..28286334-chr3:28300676..28304694,4	K562	blood:
5	chr3:28279814..28285757-chr3:28388127..28392208,14	K562	blood:

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction
ENSG00000206559	Chromatin interaction
ENSG00000163512	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11706332	0.85[CHB][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap]
rs11708424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11720107	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs11918050	0.84[CHB][hapmap]
rs11921692	0.84[CHB][hapmap]
rs11921943	0.85[CHB][hapmap]
rs12107256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13081520	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13082167	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs13083544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13085075	0.85[CHB][hapmap]
rs13085245	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13087143	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13087774	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13090439	0.85[CHB][hapmap]
rs13092618	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13093242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13095628	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs13095675	0.85[CHB][hapmap]
rs13099152	0.81[ASN][1000 genomes]
rs1599826	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1606386	0.92[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1606388	0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]
rs1610238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17021221	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17021306	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17021402	0.85[CHB][hapmap]
rs17357206	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs17638742	0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs17638782	0.81[ASN][1000 genomes]
rs17638991	0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs17695765	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs17695884	0.85[CHB][hapmap]
rs17696025	0.85[CHB][hapmap]
rs1870259	0.84[CHB][hapmap]
rs2016948	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34017994	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34419916	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34541614	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34574968	0.81[ASN][1000 genomes]
rs34681294	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34748842	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35217335	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35232922	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35439056	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35460328	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35496780	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35530532	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35565264	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35575798	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35678778	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35736614	0.81[ASN][1000 genomes]
rs35768817	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35845822	0.82[ASN][1000 genomes]
rs35937120	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36105900	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs3762797	0.85[CHB][hapmap]
rs4452283	0.85[CHB][hapmap]
rs4522735	0.81[ASN][1000 genomes]
rs4680909	0.85[CHB][hapmap]
rs4680913	0.85[CHB][hapmap]
rs56946005	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62251105	0.81[ASN][1000 genomes]
rs62251108	0.83[ASN][1000 genomes]
rs62252069	0.81[ASN][1000 genomes]
rs66502736	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66716911	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67023418	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6771057	0.85[CHB][hapmap]
rs6771460	0.85[CHB][hapmap]
rs68097246	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71087683	0.81[ASN][1000 genomes]
rs7434193	0.83[CHB][hapmap]
rs7635383	0.83[ASN][1000 genomes]
rs7639750	0.85[CHB][hapmap]
rs7641491	0.85[CHB][hapmap]
rs7649498	0.85[CHB][hapmap]
rs7651883	0.85[CHB][hapmap]
rs9843464	0.85[CHB][hapmap]

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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28282000-28283800	Active TSS	Fetal Brain Female	brain
2	chr3:28282000-28283800	Active TSS	Right Ventricle	heart
3	chr3:28282000-28284000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:28282000-28284000	Active TSS	Ovary	ovary
5	chr3:28282000-28284600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:28282200-28283800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:28282200-28284200	Active TSS	Right Atrium	heart
8	chr3:28282200-28284400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:28282400-28283800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:28282400-28283800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:28282400-28283800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:28282400-28283800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:28282400-28283800	Active TSS	Fetal Muscle Leg	muscle
14	chr3:28282400-28283800	Active TSS	NHDF-Ad	bronchial
15	chr3:28282400-28284000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr3:28282400-28284000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:28282400-28284000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:28282400-28284000	Active TSS	Aorta	Aorta
19	chr3:28282400-28284000	Active TSS	Fetal Muscle Trunk	muscle
20	chr3:28282400-28284000	Active TSS	Left Ventricle	heart
21	chr3:28282400-28284200	Active TSS	Psoas Muscle	Psoas
22	chr3:28282400-28284400	Active TSS	Colonic Mucosa	Colon
23	chr3:28282400-28284400	Active TSS	Fetal Brain Male	brain
24	chr3:28282600-28283800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:28282600-28283800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:28282600-28283800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:28282600-28283800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:28282600-28283800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:28282600-28283800	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr3:28282600-28283800	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:28282600-28283800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:28282600-28283800	Active TSS	Brain Cingulate Gyrus	brain
33	chr3:28282600-28283800	Active TSS	Brain Substantia Nigra	brain
34	chr3:28282600-28283800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr3:28282600-28283800	Active TSS	Fetal Heart	heart
36	chr3:28282600-28283800	Active TSS	Lung	lung
37	chr3:28282600-28283800	Active TSS	Pancreas	Pancrea
38	chr3:28282600-28283800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr3:28282600-28284000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:28282600-28284000	Active TSS	Esophagus	oesophagus
41	chr3:28282600-28284000	Active TSS	Fetal Intestine Small	intestine
42	chr3:28282600-28284000	Active TSS	Fetal Lung	lung
43	chr3:28282600-28284000	Active TSS	Gastric	stomach
44	chr3:28282600-28284000	Active TSS	Rectal Smooth Muscle	rectum
45	chr3:28282600-28284000	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr3:28282600-28284000	Active TSS	Small Intestine	intestine
47	chr3:28282600-28284000	Active TSS	Stomach Smooth Muscle	stomach
48	chr3:28282600-28284000	Active TSS	GM12878-XiMat	blood
49	chr3:28282600-28284000	Active TSS	HSMMtube	muscle
50	chr3:28282600-28284200	Active TSS	iPS-20b Cell Line	embryonic stem cell

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