Variant report

Variant	rs2490128
Chromosome Location	chr6:48733552-48733553
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:47755654..47756833-chr6:48732471..48733620,5	MCF-7	breast:
2	chr6:47755503..47756331-chr6:48732735..48733661,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10807397	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938183	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1938226	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2186213	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2490133	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2495862	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2495880	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2495881	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2495884	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2495885	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2495887	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4144035	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4316002	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4443509	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369811	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9473468	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1033151	chr6:48067287-48797029	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv538217	chr6:48067287-48797029	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv949690	chr6:48595821-49289855	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2490128	DEFB113	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:48730400-48733800	Enhancers	Fetal Lung	lung
2	chr6:48731400-48735800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:48732000-48733600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:48732000-48733800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr6:48732000-48733800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:48732000-48734200	Enhancers	Hela-S3	cervix
7	chr6:48732000-48734800	Enhancers	NHEK	skin
8	chr6:48732000-48735000	Enhancers	NHLF	lung
9	chr6:48732200-48733600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:48732200-48733800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:48732200-48734200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:48732200-48734800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:48732400-48733600	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr6:48732400-48734800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:48732600-48733600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:48732600-48733800	Enhancers	Stomach Mucosa	stomach
17	chr6:48732800-48734800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:48732800-48735000	Enhancers	HMEC	breast
19	chr6:48733000-48734200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:48733000-48734200	Enhancers	NH-A	brain
21	chr6:48733000-48735600	Weak transcription	Fetal Brain Male	brain
22	chr6:48733200-48733800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:48733200-48734000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr6:48733200-48734800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:48733200-48734800	Enhancers	A549	lung
26	chr6:48733400-48734000	Enhancers	Fetal Intestine Large	intestine
27	chr6:48733400-48734400	Enhancers	HSMM	muscle
28	chr6:48733400-48734800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:48733400-48734800	Enhancers	Osteobl	bone
30	chr6:48733400-48735000	Enhancers	NHDF-Ad	bronchial

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