Variant report

Variant	rs12511861
Chromosome Location	chr4:76936098-76936099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76931323..76934256-chr4:76935790..76937380,2	K562	blood:

Variant related genes	Relation type
ENSG00000156219	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10019066	1.00[JPT][hapmap]
rs10222911	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1050176	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10856871	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097192	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12499668	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12500200	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12504915	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12509988	0.83[CEU][hapmap]
rs12509996	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12511352	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12511357	0.80[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12511359	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13106039	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs1554015	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17001275	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17001284	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1910907	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2869461	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28703679	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733236	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4621456	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4859412	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55964684	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56039229	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56105413	0.90[EUR][1000 genomes]
rs56316945	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58909712	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59559903	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61279846	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532084	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532167	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6532168	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs6532169	0.83[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs6532170	0.83[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs66477189	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67210456	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67297326	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67413521	0.85[ASN][1000 genomes]
rs67687266	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6828744	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6834291	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847716	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857358	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72651379	0.82[EUR][1000 genomes]
rs72651387	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7349626	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7666094	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs7670156	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7671125	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7679689	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7685390	0.83[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7692605	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs7693606	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs7696286	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9998233	0.83[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12511861	NAAA	cis	lymphoblastoid	seeQTL
rs12511861	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs12511861	ASAHL	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76933000-76937400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:76933000-76937600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:76933000-76937600	Weak transcription	Placenta	Placenta
4	chr4:76933000-76937600	Weak transcription	Pancreas	Pancrea
5	chr4:76933400-76936200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr4:76933400-76936200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:76933400-76937600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:76933600-76937400	Weak transcription	Fetal Thymus	thymus
9	chr4:76933600-76937600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:76933800-76937600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:76934000-76936800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:76934000-76937200	Enhancers	GM12878-XiMat	blood
13	chr4:76934000-76938000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:76934200-76936400	Enhancers	Fetal Intestine Large	intestine
15	chr4:76934400-76937400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:76934400-76937400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:76934400-76937400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:76934400-76937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:76934400-76937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:76934400-76944200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:76934600-76937400	Weak transcription	HMEC	breast
22	chr4:76934600-76937400	Weak transcription	NHEK	skin
23	chr4:76935000-76937600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:76935400-76937800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:76935800-76936600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:76936000-76936200	Enhancers	Primary B cells from cord blood	blood
27	chr4:76936000-76937200	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr4:76936000-76938400	Weak transcription	Fetal Intestine Small	intestine

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