Variant report

Variant	rs13083544
Chromosome Location	chr3:28289476-28289477
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:28282357..28285690-chr3:28288463..28290366,3	MCF-7	breast:
2	chr3:28216893..28219408-chr3:28288300..28290033,2	MCF-7	breast:
3	chr3:28289132..28291586-chr3:28300746..28303472,2	K562	blood:

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11706332	0.85[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.85[ASN][1000 genomes]
rs11708424	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720107	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs11918050	0.84[CHB][hapmap]
rs11921692	0.84[CHB][hapmap]
rs11921943	0.85[CHB][hapmap]
rs12107256	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13081520	0.85[CHB][hapmap];0.83[MEX][hapmap]
rs13082167	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13085075	0.85[CHB][hapmap]
rs13085245	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13087143	0.85[CHB][hapmap];0.83[MEX][hapmap]
rs13087774	0.85[CHB][hapmap];0.83[MEX][hapmap]
rs13090296	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]
rs13090439	0.85[CHB][hapmap]
rs13092618	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13093242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13095628	0.85[CHB][hapmap];0.89[MEX][hapmap]
rs13095675	0.85[CHB][hapmap]
rs13099152	0.87[ASN][1000 genomes]
rs1585211	0.85[CHB][hapmap]
rs1599826	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1606386	0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1606388	0.92[CHB][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs1610238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17021221	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17021306	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17021402	0.85[CHB][hapmap]
rs17357206	0.85[CHB][hapmap];0.83[MEX][hapmap]
rs17638742	0.92[CHB][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs17638782	0.87[ASN][1000 genomes]
rs17638991	0.85[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs17695765	0.85[CHB][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs17695884	0.85[CHB][hapmap]
rs17696025	0.85[CHB][hapmap]
rs1870259	0.84[CHB][hapmap]
rs2016948	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34017994	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34419916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34541614	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34574968	0.86[ASN][1000 genomes]
rs34681294	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34748842	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35217335	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35232922	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35439056	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35460328	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35496780	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35530532	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35565264	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35575798	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35678778	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35736614	0.87[ASN][1000 genomes]
rs35768817	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35845822	0.88[ASN][1000 genomes]
rs35937120	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36105900	0.85[CHB][hapmap];0.83[MEX][hapmap]
rs3762797	0.85[CHB][hapmap]
rs4452283	0.85[CHB][hapmap]
rs4522735	0.87[ASN][1000 genomes]
rs4680909	0.85[CHB][hapmap]
rs4680913	0.85[CHB][hapmap]
rs56946005	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62251105	0.86[ASN][1000 genomes]
rs62251108	0.84[ASN][1000 genomes]
rs62252069	0.87[ASN][1000 genomes]
rs66502736	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66716911	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67023418	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771057	0.85[CHB][hapmap]
rs6771460	0.85[CHB][hapmap]
rs68097246	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71087683	0.87[ASN][1000 genomes]
rs7434193	0.83[CHB][hapmap]
rs7635383	0.89[ASN][1000 genomes]
rs7639750	0.85[CHB][hapmap]
rs7641491	0.85[CHB][hapmap]
rs7649498	0.85[CHB][hapmap]
rs7650831	0.83[ASN][1000 genomes]
rs7651883	0.85[CHB][hapmap]
rs952888	0.85[ASN][1000 genomes]
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:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28283800-28311400	Weak transcription	Lung	lung
2	chr3:28284000-28290000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:28284000-28290800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:28284000-28304800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:28284000-28309600	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:28284000-28313800	Weak transcription	Ovary	ovary
7	chr3:28284000-28317200	Weak transcription	Gastric	stomach
8	chr3:28284200-28292600	Weak transcription	Psoas Muscle	Psoas
9	chr3:28284200-28292800	Weak transcription	Small Intestine	intestine
10	chr3:28284400-28291400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:28284400-28292200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:28284400-28293600	Weak transcription	Right Ventricle	heart
13	chr3:28284400-28305400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:28284400-28305800	Weak transcription	Hela-S3	cervix
15	chr3:28284400-28311000	Weak transcription	Fetal Intestine Small	intestine
16	chr3:28284400-28312600	Weak transcription	Fetal Lung	lung
17	chr3:28284400-28321800	Weak transcription	NHLF	lung
18	chr3:28284600-28291600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:28284600-28292200	Weak transcription	NHEK	skin
20	chr3:28284600-28292400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:28284600-28293400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:28284600-28305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:28284600-28306000	Weak transcription	A549	lung
24	chr3:28284600-28307200	Weak transcription	Fetal Intestine Large	intestine
25	chr3:28284600-28311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:28285200-28305200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:28285200-28305600	Weak transcription	Fetal Thymus	thymus
28	chr3:28285400-28294000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:28285600-28290200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:28285600-28315400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:28285800-28305400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:28285800-28311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:28286000-28290200	Weak transcription	Placenta	Placenta
34	chr3:28286000-28292200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:28286000-28292600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:28286000-28294000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:28286000-28306000	Weak transcription	K562	blood
38	chr3:28286000-28307200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:28286200-28291400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:28286200-28294400	Weak transcription	Spleen	Spleen
41	chr3:28286400-28291200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:28287200-28289600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr3:28287200-28304800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:28287600-28317000	Weak transcription	Pancreas	Pancrea
45	chr3:28287800-28290000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:28288000-28293200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr3:28288200-28293600	Weak transcription	HepG2	liver
48	chr3:28288400-28290200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:28288600-28293800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:28288600-28305200	Weak transcription	Liver	Liver

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