Variant report

Variant	rs2490637
Chromosome Location	chr13:50545357-50545358
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50543750..50545594-chr13:50547899..50550003,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2066550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2472395	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2476389	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2476391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2490636	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2490638	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2490639	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34047395	0.82[EUR][1000 genomes]
rs706609	0.82[EUR][1000 genomes]
rs706615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs706617	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[TSI][hapmap];0.82[EUR][1000 genomes]
rs73489867	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs790528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs790529	0.82[EUR][1000 genomes]
rs790530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs790531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs790532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs790928	0.82[EUR][1000 genomes]
rs790931	0.82[EUR][1000 genomes]
rs790934	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs790935	0.80[EUR][1000 genomes]
rs790937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs790939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs790941	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	nsv561630	chr13:50525141-50545402	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv517142	chr13:50535863-50545357	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50522400-50550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:50529400-50547000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr13:50529600-50550000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr13:50530000-50546600	Weak transcription	Fetal Thymus	thymus
5	chr13:50531400-50550400	Weak transcription	NHDF-Ad	bronchial
6	chr13:50533000-50552200	Weak transcription	Ovary	ovary
7	chr13:50534400-50550400	Weak transcription	HSMM	muscle
8	chr13:50535600-50547400	Weak transcription	Thymus	Thymus
9	chr13:50536400-50552800	Weak transcription	Fetal Heart	heart
10	chr13:50538200-50550400	Weak transcription	Brain Substantia Nigra	brain
11	chr13:50538200-50558000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr13:50538800-50550400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:50539000-50548800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr13:50539000-50570000	Weak transcription	Fetal Intestine Small	intestine
15	chr13:50539800-50550400	Weak transcription	A549	lung
16	chr13:50540000-50550400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr13:50540200-50562200	Weak transcription	Adipose Nuclei	Adipose
18	chr13:50540400-50547200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr13:50540400-50550400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr13:50540400-50550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:50540400-50569800	Weak transcription	Primary T cells from cord blood	blood
22	chr13:50540600-50549400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:50541200-50546800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:50542600-50550800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr13:50543400-50547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr13:50543600-50570400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:50544000-50547000	Weak transcription	Pancreas	Pancrea
28	chr13:50544000-50549200	Weak transcription	Osteobl	bone
29	chr13:50544800-50545400	Strong transcription	Fetal Muscle Leg	muscle
30	chr13:50544800-50545400	Strong transcription	Skeletal Muscle Male	skeletal muscle

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