Variant report

Variant	rs11130126
Chromosome Location	chr3:47306894-47306895
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	chr3:47306715..47308916-chr3:47322571..47324674,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114648	Chromatin interaction
ENSG00000088727	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1038394	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs10490798	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1076394	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs10865946	0.88[CEU][hapmap]
rs11130115	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs11130123	0.89[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs11130124	0.92[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs11130128	0.88[CEU][hapmap]
rs11130129	0.87[CEU][hapmap]
rs11705957	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs11710013	0.92[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11710121	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11710322	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs11711824	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs11712445	0.91[CEU][hapmap]
rs11714294	0.85[EUR][1000 genomes]
rs11719877	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs11720439	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11915074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11920354	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11920853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11921117	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11925560	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12631730	0.90[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs12636851	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs13061071	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs13075233	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs13094438	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs1466740	0.90[AFR][1000 genomes]
rs1466741	0.83[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1531875	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs1638676	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs17410853	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs17411375	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs17476234	0.87[EUR][1000 genomes]
rs1872164	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs2088135	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2101247	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs2132173	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs2159400	0.92[CEU][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap]
rs2240796	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2276853	0.92[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2276854	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs295428	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs295441	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs295442	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs295449	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs295458	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs295461	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs3736177	0.87[CEU][hapmap]
rs4078466	0.89[TSI][hapmap]
rs4082155	0.89[TSI][hapmap]
rs4682852	0.82[CEU][hapmap]
rs4683326	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4858811	0.88[CEU][hapmap]
rs4858824	0.88[CEU][hapmap]
rs4858868	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs4858893	0.88[CEU][hapmap]
rs4858894	0.82[CEU][hapmap]
rs56250009	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57756484	0.83[AFR][1000 genomes]
rs58472056	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61386020	0.85[ASN][1000 genomes]
rs62246455	0.83[AFR][1000 genomes]
rs62248905	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6767907	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6768221	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6772670	0.91[CEU][hapmap]
rs6773521	0.83[AFR][1000 genomes]
rs6780013	0.96[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs6781941	0.83[AFR][1000 genomes]
rs6791842	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs6792461	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs6800271	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs73069104	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7433300	0.92[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap]
rs7632501	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636423	0.90[EUR][1000 genomes]
rs7651762	0.88[CEU][hapmap]
rs807932	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs807935	0.85[EUR][1000 genomes]
rs807936	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs807937	0.86[EUR][1000 genomes]
rs811115	0.91[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs878659	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs922957	0.88[CEU][hapmap]
rs9311403	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9683033	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs9837343	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs9845728	0.81[AFR][1000 genomes]
rs9854790	0.81[AFR][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11130126	PRKAR2A	cis	cerebellum	SCAN
rs11130126	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11130126	HYAL2	cis	cerebellum	SCAN
rs11130126	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11130126	NCKIPSD	cis	cerebellum	SCAN
rs11130126	C3orf75	cis	cerebellum	SCAN
rs11130126	SCAP	cis	parietal	SCAN
rs11130126	DHX30	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47264200-47322200	Weak transcription	Gastric	stomach
2	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:47285400-47315800	Weak transcription	Pancreas	Pancrea
7	chr3:47285600-47312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
9	chr3:47299400-47308200	Weak transcription	Right Atrium	heart
10	chr3:47299600-47307800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:47300800-47322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:47301000-47322800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:47301200-47323000	Weak transcription	Psoas Muscle	Psoas
14	chr3:47302200-47308000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:47302400-47307200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:47302600-47314600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:47302600-47322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:47302800-47323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:47303200-47308400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:47303400-47307000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:47303400-47308000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:47303400-47308000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:47305200-47307200	Strong transcription	Brain Anterior Caudate	brain
24	chr3:47305600-47323200	Weak transcription	Primary T cells from cord blood	blood
25	chr3:47305800-47315000	Weak transcription	Fetal Intestine Small	intestine
26	chr3:47306000-47308400	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:47306600-47307000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr3:47306600-47308200	Enhancers	K562	blood
29	chr3:47306600-47309000	Enhancers	Fetal Muscle Leg	muscle
30	chr3:47306600-47309000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:47306600-47309000	Enhancers	GM12878-XiMat	blood
32	chr3:47306800-47307000	ZNF genes & repeats	Lung	lung
33	chr3:47306800-47307200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:47306800-47309000	Enhancers	HSMM	muscle
35	chr3:47306800-47309200	Enhancers	HSMMtube	muscle
36	chr3:47306800-47310000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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