Variant report

Variant	rs4953729
Chromosome Location	chr2:110331887-110331888
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	chr2:110321272..110323476-chr2:110330973..110332963,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10195867	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036317	1.00[ASN][1000 genomes]
rs1036318	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10496432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006297	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412327	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811388	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28464093	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28553892	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28599496	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28696274	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3213866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34111852	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34269507	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34311530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34441132	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34517320	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34821058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35120088	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35223862	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35392016	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531839	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35550721	1.00[ASN][1000 genomes]
rs35955221	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4482487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953721	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953730	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953847	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953848	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953849	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953853	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs55794045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56794190	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58031484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594050	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6709945	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719215	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737736	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6751785	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72824772	0.89[EUR][1000 genomes]
rs72824788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824789	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72824796	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824800	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565483	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330317	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330321	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750931	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9751648	0.85[EUR][1000 genomes]
rs9752531	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9798179	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv2874	chr2:110289373-110333621	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293400-110352200	Weak transcription	Gastric	stomach
2	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
6	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
8	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
10	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
11	chr2:110310400-110337800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:110310400-110338400	Weak transcription	Lung	lung
13	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
16	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:110310800-110336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:110313400-110337000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:110318200-110338000	Weak transcription	NHEK	skin
22	chr2:110318200-110348400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
24	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:110321200-110332800	Weak transcription	Fetal Heart	heart
27	chr2:110323400-110332600	Weak transcription	Brain Substantia Nigra	brain
28	chr2:110323400-110343800	Weak transcription	Aorta	Aorta
29	chr2:110323400-110348000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:110323400-110348200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:110323600-110341000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:110323600-110344200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:110324000-110337400	Weak transcription	Fetal Intestine Small	intestine
34	chr2:110324000-110342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:110324000-110348400	Weak transcription	Hela-S3	cervix
36	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
37	chr2:110324200-110342800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:110324200-110348600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:110324600-110362200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:110325200-110341000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:110325400-110343800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:110325800-110342800	Weak transcription	A549	lung
43	chr2:110327400-110336600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:110328400-110332400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:110328400-110332400	Strong transcription	Fetal Intestine Large	intestine
46	chr2:110328400-110333000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:110328400-110336400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:110328800-110349000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:110329000-110369000	Weak transcription	Ovary	ovary
50	chr2:110329200-110341200	Weak transcription	Fetal Kidney	kidney

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