Variant report

Variant	rs508405
Chromosome Location	chr2:30980940-30980941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30980803..30983163-chr2:30994133..30996203,2	MCF-7	breast:
2	chr2:30977562..30982184-chr2:31026694..31034377,7	MCF-7	breast:
3	chr2:30980741..30983020-chr2:30986437..30988713,2	K562	blood:
4	chr2:30978882..30982474-chr2:30994656..30997998,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162949	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1402048	0.84[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2609932	0.94[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs2681676	1.00[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926303	0.89[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs482384	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs485100	0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs546987	0.81[EUR][1000 genomes]
rs939368	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv873770	chr2:30952987-30984850	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv520269	chr2:30958137-30988375	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv456019	chr2:30968228-30984850	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv581267	chr2:30968228-30984850	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs508405	SLC30A3	cis	parietal	SCAN
rs508405	RBKS	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30965800-30999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:30968200-30985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:30971000-30984800	Weak transcription	Stomach Mucosa	stomach
4	chr2:30978400-30981200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:30978600-30984600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:30979200-30981600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:30979600-30981400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr2:30979600-30985000	Weak transcription	Fetal Intestine Small	intestine
9	chr2:30979600-30985400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:30980000-30981000	Strong transcription	Gastric	stomach
11	chr2:30980000-30981200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:30980400-30981000	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:30980400-30981600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
14	chr2:30980600-30981400	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr2:30980600-30981600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr2:30980600-30981600	Enhancers	NHDF-Ad	bronchial
17	chr2:30980600-30983800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:30980800-30981000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:30980800-30988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:30980800-31003600	Weak transcription	Pancreas	Pancrea
21	chr2:30980800-31019800	Weak transcription	Brain Hippocampus Middle	brain

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