Variant report

Variant	rs4952591
Chromosome Location	chr2:40425544-40425545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40419927..40421772-chr2:40425195..40428157,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1019781	0.85[AMR][1000 genomes]
rs10490208	0.83[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11674102	0.94[CHB][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11690292	0.83[JPT][hapmap]
rs11691096	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12104840	0.88[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13390338	0.83[JPT][hapmap]
rs17503184	0.82[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs17504446	0.83[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs17504670	0.87[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs35963830	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828295	0.83[JPT][hapmap]
rs4624433	0.83[ASN][1000 genomes]
rs4952401	0.91[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs4952532	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4952594	0.88[JPT][hapmap]
rs62148765	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6734847	0.83[JPT][hapmap]
rs7558668	0.84[AMR][1000 genomes]
rs7558770	0.83[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs7558787	0.83[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs918050	0.82[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2763455	chr2:40416373-40433420	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1001866	chr2:40416373-40433420	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv581503	chr2:40417012-40430611	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv581504	chr2:40418386-40430611	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv526425	chr2:40418386-40447587	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv526074	chr2:40423454-40451724	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40400600-40426800	Weak transcription	Osteobl	bone
2	chr2:40405400-40430000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:40416000-40425800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:40417200-40430400	Weak transcription	Aorta	Aorta
5	chr2:40418200-40447200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:40418600-40445800	Weak transcription	Dnd41	blood
7	chr2:40419200-40436600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:40420400-40426200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:40420600-40430000	Weak transcription	NHLF	lung
10	chr2:40420800-40428800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:40421200-40429200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:40422000-40435200	Weak transcription	Fetal Kidney	kidney
13	chr2:40422200-40430000	Weak transcription	Left Ventricle	heart
14	chr2:40422600-40436400	Weak transcription	Right Ventricle	heart
15	chr2:40423600-40426800	Enhancers	HSMM	muscle
16	chr2:40424000-40427000	Genic enhancers	Fetal Heart	heart
17	chr2:40424600-40430000	Weak transcription	Fetal Brain Male	brain
18	chr2:40424600-40430400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:40424800-40426400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:40424800-40426800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:40424800-40429800	Weak transcription	Fetal Brain Female	brain
22	chr2:40425000-40425800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:40425200-40425800	Weak transcription	HSMMtube	muscle
24	chr2:40425200-40426400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:40425200-40430000	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:40425400-40433400	Weak transcription	Primary monocytes fromperipheralblood	blood

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