Variant report

Variant	rs12786563
Chromosome Location	chr11:66179556-66179557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66178617..66182846-chr11:66233646..66237657,3	MCF-7	breast:
2	chr11:66175058..66178321-chr11:66178866..66181551,3	K562	blood:

Variant related genes	Relation type
ENSG00000254510	Chromatin interaction
ENSG00000174516	Chromatin interaction
ENSG00000174547	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1039594	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1047029	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10750784	0.96[CEU][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10791869	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10791872	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10791874	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10791876	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896111	0.96[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10896112	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10896115	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10896116	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227465	0.86[EUR][1000 genomes]
rs11601396	0.86[EUR][1000 genomes]
rs11823140	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs12416747	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12576299	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12577196	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12577917	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs12785321	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12785651	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12794121	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1546358	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1784029	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs1785633	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1785639	0.92[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs1892940	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes]
rs2236679	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2279861	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279862	0.83[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2282530	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282531	0.96[CEU][hapmap]
rs3016767	0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3177514	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34043951	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244813	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4466842	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930177	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930178	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4930179	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930181	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930360	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4930362	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930363	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930366	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55998145	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56123976	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56321771	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61891449	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591213	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6591215	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6591217	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66810040	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7104253	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7104570	0.96[CEU][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7105015	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105401	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107191	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7110944	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7117630	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126018	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73489638	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7938676	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7939111	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7940980	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs905770	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs947978	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[EUR][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	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
3	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active 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	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12786563	OVOL1	cis	parietal	SCAN
rs12786563	ASRGL1	cis	parietal	SCAN
rs12786563	SLC25A45	cis	parietal	SCAN
rs12786563	RIN1	cis	Whole Blood	GTEx
rs12786563	B3GNT1	cis	parietal	SCAN
rs12786563	ACTN3	cis	Muscle Skeletal	GTEx
rs12786563	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs12786563	ALDH3B1	cis	parietal	SCAN
rs12786563	CCDC87	cis	parietal	SCAN
rs12786563	ESRRA	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66176600-66179800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr11:66177000-66180200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr11:66177000-66180600	Weak transcription	Fetal Brain Male	brain
4	chr11:66177000-66181000	Weak transcription	Spleen	Spleen
5	chr11:66177000-66181800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:66177000-66183600	Weak transcription	Right Atrium	heart
7	chr11:66177200-66179600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:66177200-66180000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:66177200-66180000	Active TSS	Colon Smooth Muscle	Colon
10	chr11:66177200-66180600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:66177400-66180800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:66177400-66181000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:66177400-66185000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:66177600-66180400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:66177600-66181400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:66177600-66184600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:66178000-66183000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:66178200-66180200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:66178200-66180400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr11:66178600-66179600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr11:66178600-66179800	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr11:66178600-66180200	Bivalent/Poised TSS	Fetal Stomach	stomach
23	chr11:66178800-66179600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
24	chr11:66179000-66179800	Bivalent Enhancer	Fetal Brain Female	brain
25	chr11:66179000-66180000	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr11:66179200-66185200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:66179400-66179800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:66179400-66179800	Active TSS	Rectal Smooth Muscle	rectum
29	chr11:66179400-66180200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:66179400-66180800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:66179400-66180800	Enhancers	Fetal Heart	heart
32	chr11:66179400-66181200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:66179400-66185000	Weak transcription	Aorta	Aorta
34	chr11:66179400-66185200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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