Variant report

Variant	rs4952843
Chromosome Location	chr2:46957845-46957846
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	chr2:46925799..46928213-chr2:46954632..46957949,3	MCF-7	breast:
2	chr2:46933207..46934969-chr2:46956262..46957915,2	K562	blood:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1058157	0.80[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109380	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11676737	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11695058	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12474201	0.80[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes]
rs12998753	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12998762	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12999586	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13025595	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13025984	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13429704	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17822019	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17822294	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346878	0.84[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34401107	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35158352	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35722922	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35825831	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829835	0.80[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4952842	0.80[CEU][hapmap];0.89[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4953419	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6738426	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7562173	0.96[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594523	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs897530	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46945400-46985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:46947600-46975600	Weak transcription	HSMM	muscle
3	chr2:46948200-46962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:46948200-46964400	Weak transcription	NHEK	skin
5	chr2:46948200-46967400	Weak transcription	Esophagus	oesophagus
6	chr2:46948200-46974600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:46948200-46977200	Weak transcription	Aorta	Aorta
8	chr2:46948400-46961600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:46948600-46964200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:46948600-46964400	Weak transcription	NH-A	brain
11	chr2:46948600-46974400	Weak transcription	Fetal Stomach	stomach
12	chr2:46949600-46958400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:46950800-46958200	Weak transcription	NHLF	lung
14	chr2:46950800-46975400	Weak transcription	Fetal Lung	lung
15	chr2:46951400-46962200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:46951800-46959000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:46952000-46961800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:46952600-46962000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:46953400-46964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:46955000-46958000	Weak transcription	Fetal Intestine Small	intestine
21	chr2:46955000-46975400	Weak transcription	Small Intestine	intestine
22	chr2:46955200-46958000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:46955200-46958000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:46955200-46958600	Weak transcription	Primary T cells from cord blood	blood
25	chr2:46955200-46958600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:46955200-46958600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:46955200-46959400	Weak transcription	HepG2	liver
28	chr2:46955200-46961800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:46955200-46964600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:46955200-46967600	Weak transcription	Thymus	Thymus
31	chr2:46955200-46970400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:46955200-46974400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:46955200-46984800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr2:46955200-46985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:46955400-46958000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:46955400-46958200	Weak transcription	A549	lung
37	chr2:46955400-46958400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:46955400-46959400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:46955400-46962000	Weak transcription	Liver	Liver
40	chr2:46955400-46962000	Weak transcription	Pancreas	Pancrea
41	chr2:46955400-46962000	Weak transcription	Psoas Muscle	Psoas
42	chr2:46955400-46962000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:46955400-46967600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:46955400-46967800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:46955400-46967800	Weak transcription	Fetal Thymus	thymus
46	chr2:46955400-46974200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:46955600-46959000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:46955600-46959000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:46955600-46959400	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:46956000-46959000	Weak transcription	Ovary	ovary

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