Variant report

Variant	rs13424717
Chromosome Location	chr2:46995893-46995894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46990483..46993440-chr2:46995579..46997950,2	MCF-7	breast:
2	chr2:46993693..46996690-chr2:47027722..47029756,2	MCF-7	breast:
3	chr2:46995520..46997154-chr2:47000594..47003342,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10182163	0.86[GIH][hapmap]
rs10187320	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10192254	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10196768	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10204610	1.00[ASN][1000 genomes]
rs10221923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10439427	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10439469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151534	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12329330	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13391877	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13402099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13412085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13420535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421701	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13426735	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13432741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770970	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17771838	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35750425	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46981400-47006800	Weak transcription	Psoas Muscle	Psoas
2	chr2:46984400-46998600	Weak transcription	Fetal Brain Male	brain
3	chr2:46985600-46998600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:46985600-47008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:46987200-46996200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:46987200-46997800	Weak transcription	Liver	Liver
7	chr2:46987400-46997000	Weak transcription	Fetal Lung	lung
8	chr2:46987400-46997400	Weak transcription	Fetal Stomach	stomach
9	chr2:46987400-46997600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:46987400-46997600	Weak transcription	Fetal Intestine Small	intestine
11	chr2:46987400-47005600	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:46987400-47005600	Weak transcription	Left Ventricle	heart
13	chr2:46987600-46997000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:46987600-46997200	Weak transcription	HSMM	muscle
15	chr2:46987600-46997400	Weak transcription	Fetal Intestine Large	intestine
16	chr2:46987600-47006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:46987800-46997200	Weak transcription	NH-A	brain
18	chr2:46988200-46997400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:46989400-46997200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:46991600-46997200	Weak transcription	Ovary	ovary
21	chr2:46992000-46997000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:46992200-46997000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:46992200-46997000	Weak transcription	NHLF	lung
24	chr2:46992400-47005400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:46993200-46997600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:46995000-46996000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:46995000-46997000	Weak transcription	HepG2	liver
28	chr2:46995000-46999000	Enhancers	Osteobl	bone
29	chr2:46995200-46997000	Enhancers	A549	lung
30	chr2:46995200-46999000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:46995600-46996000	Enhancers	NHDF-Ad	bronchial
32	chr2:46995600-46996200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:46995800-46997800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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