Variant report

Variant	rs12576878
Chromosome Location	chr11:57098696-57098697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57098379-57098721	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:57098328-57098710	K562	blood:	n/a	n/a
3	POLR2A	chr11:57098265-57098732	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000238692	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10792086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792089	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792091	0.92[ASN][1000 genomes]
rs10896598	0.92[ASN][1000 genomes]
rs10896603	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896604	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs10896605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896608	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs11228995	0.92[ASN][1000 genomes]
rs11228997	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs11229003	0.92[ASN][1000 genomes]
rs11229011	0.92[ASN][1000 genomes]
rs11602265	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602266	0.92[ASN][1000 genomes]
rs11603691	0.92[ASN][1000 genomes]
rs11607950	0.92[ASN][1000 genomes]
rs12365472	0.92[ASN][1000 genomes]
rs1815769	0.92[ASN][1000 genomes]
rs2230649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135716	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938863	1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs4938864	0.92[ASN][1000 genomes]
rs61888886	0.92[ASN][1000 genomes]
rs61888887	0.92[ASN][1000 genomes]
rs61888888	0.92[ASN][1000 genomes]
rs7106462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs7111339	0.92[ASN][1000 genomes]
rs7129491	1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs7951793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv541048	chr11:57076815-57120781	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12576878	TIMM10	cis	parietal	SCAN
rs12576878	PRPF19	cis	cerebellum	SCAN
rs12576878	OR5A1	cis	cerebellum	SCAN
rs12576878	OR8I2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57093200-57101600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:57093200-57102800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:57093400-57102000	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr11:57093600-57101400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:57093600-57101600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:57093600-57102000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:57093800-57098800	Genic enhancers	Dnd41	blood
8	chr11:57093800-57100400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:57093800-57100600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:57093800-57100800	Strong transcription	Brain Cingulate Gyrus	brain
11	chr11:57093800-57100800	Strong transcription	HSMMtube	muscle
12	chr11:57093800-57101000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:57093800-57101000	Strong transcription	Brain Angular Gyrus	brain
14	chr11:57093800-57101000	Strong transcription	Brain Hippocampus Middle	brain
15	chr11:57093800-57101200	Strong transcription	Fetal Brain Female	brain
16	chr11:57093800-57101600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:57093800-57101600	Strong transcription	Brain Anterior Caudate	brain
18	chr11:57093800-57101800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:57093800-57102000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:57094000-57100000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:57094000-57100400	Strong transcription	Brain Germinal Matrix	brain
22	chr11:57094000-57100800	Strong transcription	Colon Smooth Muscle	Colon
23	chr11:57094000-57101000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr11:57094000-57101200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:57094000-57101200	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr11:57094000-57101200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr11:57094000-57101200	Strong transcription	NH-A	brain
28	chr11:57094000-57101200	Strong transcription	Osteobl	bone
29	chr11:57094000-57101400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:57094000-57101600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:57094000-57101600	Strong transcription	Fetal Muscle Leg	muscle
32	chr11:57094000-57101800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:57094000-57101800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:57094000-57101800	Strong transcription	Fetal Lung	lung
35	chr11:57094000-57101800	Strong transcription	NHEK	skin
36	chr11:57094000-57102000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:57094200-57100400	Strong transcription	NHLF	lung
38	chr11:57094200-57100800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:57094200-57100800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:57094200-57100800	Strong transcription	Brain Substantia Nigra	brain
41	chr11:57094200-57101000	Strong transcription	Primary B cells from cord blood	blood
42	chr11:57094200-57101200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr11:57094200-57101200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr11:57094200-57101400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr11:57094200-57101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:57094200-57101400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:57094200-57101600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:57094200-57101800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:57094200-57101800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr11:57094200-57102000	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links