Variant report

Variant	rs12541318
Chromosome Location	chr8:11594970-11594971
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	chr8:11594028..11596357-chr8:11603341..11605570,2	K562	blood:
2	chr8:11587952..11589513-chr8:11592423..11595406,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10503426	1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11250163	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11250164	0.85[CHB][hapmap]
rs11784693	0.85[CHB][hapmap]
rs12541921	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12550668	1.00[LWK][hapmap]
rs13250578	0.82[CHB][hapmap]
rs13259242	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2409836	0.82[CEU][hapmap]
rs2898295	0.82[MEX][hapmap]
rs34421088	0.96[ASN][1000 genomes]
rs34962960	1.00[ASN][1000 genomes]
rs35558975	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4841600	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12541318	DEFB134	cis	cerebellum	SCAN
rs12541318	MFHAS1	cis	cerebellum	SCAN
rs12541318	C8orf13	cis	multi-tissue	Pritchard
rs12541318	PPP1R3B	cis	cerebellum	SCAN
rs12541318	PRSS55	cis	cerebellum	SCAN
rs12541318	CTSB	cis	cerebellum	SCAN
rs12541318	FLJ10661	cis	cerebellum	SCAN
rs12541318	CLDN23	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11591800-11597400	Enhancers	Fetal Heart	heart
2	chr8:11593400-11595200	Enhancers	Fetal Intestine Large	intestine
3	chr8:11593400-11597800	Enhancers	Placenta	Placenta
4	chr8:11593400-11601400	Genic enhancers	Fetal Intestine Small	intestine
5	chr8:11593600-11595000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:11593600-11595200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:11593600-11595200	Enhancers	Small Intestine	intestine
8	chr8:11593600-11596200	Enhancers	Ovary	ovary
9	chr8:11593600-11598000	Enhancers	Left Ventricle	heart
10	chr8:11593600-11599200	Enhancers	Liver	Liver
11	chr8:11593800-11595200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:11593800-11595200	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr8:11593800-11595200	Enhancers	Pancreas	Pancrea
14	chr8:11593800-11597200	Enhancers	Right Ventricle	heart
15	chr8:11594000-11595000	Enhancers	Gastric	stomach
16	chr8:11594000-11595400	Enhancers	Colon Smooth Muscle	Colon
17	chr8:11594000-11595600	Enhancers	Stomach Mucosa	stomach
18	chr8:11594200-11595200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr8:11594200-11595200	Enhancers	Right Atrium	heart
20	chr8:11594200-11595400	Bivalent Enhancer	Adipose Nuclei	Adipose
21	chr8:11594200-11595400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr8:11594400-11595200	Enhancers	Duodenum Mucosa	Duodenum
23	chr8:11594600-11595200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr8:11594600-11595200	Bivalent Enhancer	Fetal Stomach	stomach
25	chr8:11594600-11596200	Weak transcription	HepG2	liver
26	chr8:11594600-11597200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr8:11594600-11597600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr8:11594800-11595200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr8:11594800-11595200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr8:11594800-11595200	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links