Variant report

Variant	rs6042105
Chromosome Location	chr20:13420957-13420958
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	chr20:13408378..13410884-chr20:13417652..13421238,3	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12106004	1.00[CEU][hapmap]
rs12329620	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12480266	0.88[AMR][1000 genomes]
rs12480276	0.88[AMR][1000 genomes]
rs2008702	0.82[EUR][1000 genomes]
rs2145140	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	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033699	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]
rs6033714	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6033716	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6033718	1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042061	0.96[EUR][1000 genomes]
rs6042063	0.96[EUR][1000 genomes]
rs6042068	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6042076	0.83[AMR][1000 genomes]
rs6042080	0.83[AMR][1000 genomes]
rs6042082	0.88[AMR][1000 genomes]
rs6042083	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	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042095	0.93[AMR][1000 genomes]
rs6042101	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042107	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042108	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042111	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042116	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042120	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6042123	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042130	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042136	1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6042142	1.00[YRI][hapmap];0.93[AMR][1000 genomes]
rs6042143	0.88[AMR][1000 genomes]
rs6042145	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6042154	1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105091	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105092	0.88[AMR][1000 genomes]
rs6105093	0.88[AMR][1000 genomes]
rs6105094	0.88[AMR][1000 genomes]
rs6105095	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105097	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105105	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105108	1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6105109	1.00[YRI][hapmap];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]
rs6109869	0.88[AMR][1000 genomes]
rs6109870	0.81[AMR][1000 genomes]
rs6109871	0.88[AMR][1000 genomes]
rs6109873	0.88[AMR][1000 genomes]
rs6109879	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109882	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6109883	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109885	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6109889	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109895	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109896	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6109900	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6109901	1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61151551	0.88[AMR][1000 genomes]
rs61518689	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7274078	1.00[YRI][hapmap];0.93[AMR][1000 genomes]
rs7348566	0.93[AMR][1000 genomes]
rs8119260	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8121784	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs927122	0.88[AMR][1000 genomes]
rs9653627	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv21228	chr20:13283535-13447810	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13379200-13463000	Weak transcription	HSMM	muscle
2	chr20:13392600-13421400	Weak transcription	Psoas Muscle	Psoas
3	chr20:13395600-13477800	Weak transcription	Gastric	stomach
4	chr20:13397400-13421200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr20:13399800-13430800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr20:13403800-13435000	Weak transcription	HMEC	breast
7	chr20:13404400-13434800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:13404400-13434800	Weak transcription	NHEK	skin
9	chr20:13410000-13421600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr20:13411400-13435000	Weak transcription	Lung	lung
11	chr20:13411600-13421400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr20:13412600-13421800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr20:13412600-13424200	Weak transcription	HepG2	liver
14	chr20:13413600-13433400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr20:13415200-13428000	Weak transcription	Thymus	Thymus
16	chr20:13415400-13435000	Weak transcription	Placenta	Placenta
17	chr20:13415600-13433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr20:13416000-13438200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr20:13416200-13421000	Weak transcription	Primary T cells from cord blood	blood
20	chr20:13416200-13435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:13416200-13436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr20:13416400-13434600	Weak transcription	Fetal Thymus	thymus
23	chr20:13417400-13423600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr20:13420600-13421000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
25	chr20:13420600-13421800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
26	chr20:13420600-13423000	ZNF genes & repeats	Dnd41	blood
27	chr20:13420800-13422000	ZNF genes & repeats	Primary B cells from cord blood	blood
28	chr20:13420800-13444400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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