Variant report

Variant	rs6042145
Chromosome Location	chr20:13455377-13455378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13454317..13457886-chr20:13459178..13461231,3	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs12106004	1.00[TSI][hapmap]
rs12329620	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12480266	1.00[ASW][hapmap];0.82[MEX][hapmap];0.88[AMR][1000 genomes]
rs12480276	0.88[AMR][1000 genomes]
rs13037694	1.00[ASW][hapmap]
rs1812562	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs2008702	0.82[EUR][1000 genomes]
rs2145140	1.00[ASW][hapmap];0.88[AMR][1000 genomes]
rs45489891	1.00[EUR][1000 genomes]
rs45602236	1.00[EUR][1000 genomes]
rs55940819	0.96[EUR][1000 genomes]
rs58023165	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59388287	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033699	1.00[ASW][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.88[AMR][1000 genomes]
rs6033703	0.88[AMR][1000 genomes]
rs6033704	0.88[AMR][1000 genomes]
rs6033706	0.88[AMR][1000 genomes]
rs6033708	0.88[AMR][1000 genomes]
rs6033712	0.82[MEX][hapmap]
rs6033714	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033716	0.93[AMR][1000 genomes]
rs6033718	0.82[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042061	0.96[EUR][1000 genomes]
rs6042063	0.82[CEU][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes]
rs6042068	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6042069	0.82[CEU][hapmap]
rs6042076	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs6042080	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs6042081	0.82[MEX][hapmap]
rs6042082	0.88[AMR][1000 genomes]
rs6042083	1.00[ASW][hapmap];0.88[AMR][1000 genomes]
rs6042084	0.88[AMR][1000 genomes]
rs6042086	0.88[AMR][1000 genomes]
rs6042087	0.88[AMR][1000 genomes]
rs6042089	0.88[AMR][1000 genomes]
rs6042093	0.82[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042095	0.93[AMR][1000 genomes]
rs6042101	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042105	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042107	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042108	0.82[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042111	0.82[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042116	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042120	0.93[AMR][1000 genomes]
rs6042123	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042130	0.82[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042136	1.00[ASW][hapmap];0.82[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042142	0.85[YRI][hapmap];0.93[AMR][1000 genomes]
rs6042143	0.88[AMR][1000 genomes]
rs6042151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042154	1.00[ASW][hapmap];0.82[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105082	0.82[CEU][hapmap]
rs6105083	0.82[CEU][hapmap]
rs6105091	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105092	0.88[AMR][1000 genomes]
rs6105093	0.88[AMR][1000 genomes]
rs6105094	1.00[ASW][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.88[AMR][1000 genomes]
rs6105095	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105097	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105105	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105108	0.82[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105109	0.82[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109848	0.96[EUR][1000 genomes]
rs6109849	0.88[AMR][1000 genomes]
rs6109850	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6109866	0.88[AMR][1000 genomes]
rs6109867	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109868	0.82[CEU][hapmap]
rs6109869	0.88[AMR][1000 genomes]
rs6109870	1.00[ASW][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs6109871	1.00[ASW][hapmap];0.88[AMR][1000 genomes]
rs6109872	0.82[MEX][hapmap]
rs6109873	0.88[AMR][1000 genomes]
rs6109879	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6109883	0.82[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109885	0.82[CEU][hapmap];0.93[AMR][1000 genomes]
rs6109889	0.82[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109895	1.00[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109896	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes]
rs6109900	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109901	0.82[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61151551	0.88[AMR][1000 genomes]
rs61518689	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7274078	0.82[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7348566	0.93[AMR][1000 genomes]
rs8119260	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8121784	1.00[CEU][hapmap];0.87[TSI][hapmap];0.96[EUR][1000 genomes]
rs927122	1.00[ASW][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.88[AMR][1000 genomes]
rs9653627	0.82[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13379200-13463000	Weak transcription	HSMM	muscle
2	chr20:13395600-13477800	Weak transcription	Gastric	stomach
3	chr20:13422000-13460400	Weak transcription	Primary B cells from cord blood	blood
4	chr20:13422000-13461200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr20:13430000-13467800	Weak transcription	Ovary	ovary
6	chr20:13430200-13467800	Weak transcription	Pancreas	Pancrea
7	chr20:13435400-13460400	Weak transcription	Fetal Thymus	thymus
8	chr20:13435400-13462000	Weak transcription	Left Ventricle	heart
9	chr20:13435600-13460600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr20:13436600-13458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:13436600-13460800	Weak transcription	Primary T cells from cord blood	blood
12	chr20:13442600-13461800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr20:13442600-13471600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr20:13442800-13467800	Weak transcription	Aorta	Aorta
15	chr20:13443400-13461200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr20:13445000-13460200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:13445400-13467800	Weak transcription	Fetal Stomach	stomach
18	chr20:13445600-13461000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr20:13446200-13460800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr20:13450200-13460400	Weak transcription	Fetal Lung	lung
21	chr20:13450200-13461000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr20:13450200-13461800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:13450400-13457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:13450400-13461000	Weak transcription	HepG2	liver
25	chr20:13450400-13461200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr20:13450800-13461200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr20:13451600-13464200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr20:13452000-13458400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr20:13452000-13458600	Weak transcription	Fetal Brain Male	brain
30	chr20:13452600-13460400	Weak transcription	Liver	Liver
31	chr20:13453600-13461400	Weak transcription	Fetal Kidney	kidney
32	chr20:13454200-13455400	ZNF genes & repeats	Dnd41	blood
33	chr20:13454400-13471200	Weak transcription	Small Intestine	intestine
34	chr20:13454600-13461800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr20:13454800-13460600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr20:13454800-13461800	Weak transcription	Fetal Intestine Small	intestine

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