Variant report

Variant	rs3016315
Chromosome Location	chr11:66050948-66050949
allele	A/G
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	chr11:66049874-66051187	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:66049843-66051017	K562	blood:	n/a	n/a
3	POLR2A	chr11:66050710-66050964	K562	blood:	n/a	n/a
4	POLR2A	chr11:66049870-66051017	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:66049844-66050961	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr11:66047872-66051632	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr11:66049908-66051719	A549	lung:	n/a	chr11:66050112-66050125 chr11:66050110-66050128 chr11:66050112-66050125 chr11:66050113-66050123 chr11:66050105-66050126 chr11:66050116-66050125 chr11:66050111-66050127
8	POLR2A	chr11:66049521-66051109	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr11:66049766-66051033	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr11:66049142-66052042	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr11:66048409-66051000	A549	lung:	n/a	n/a
12	CTCF	chr11:66049933-66051014	K562	blood:	n/a	chr11:66050112-66050125 chr11:66050110-66050128 chr11:66050112-66050125 chr11:66050113-66050123 chr11:66050105-66050126 chr11:66050116-66050125 chr11:66050111-66050127
13	POLR2A	chr11:66049029-66051274	SK-N-MC	brain:	n/a	n/a
14	RAD21	chr11:66049768-66050967	SK-N-SH	brain:	n/a	chr11:66050111-66050124 chr11:66050112-66050122 chr11:66050108-66050127 chr11:66049931-66049941
15	POLR2A	chr11:66048298-66051040	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr11:66048442-66051168	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:66049861-66051032	K562	blood:	n/a	n/a
18	POLR2A	chr11:66047722-66051154	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr11:66049873-66050967	GM12891	blood:	n/a	n/a
20	POLR2A	chr11:66050945-66051194	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr11:66048765-66051741	K562	blood:	n/a	n/a
22	CTCF	chr11:66050800-66050950	HVMF	connective:	n/a	n/a
23	CTCF	chr11:66049872-66051124	SK-N-SH	brain:	n/a	chr11:66050112-66050125 chr11:66050110-66050128 chr11:66050112-66050125 chr11:66050113-66050123 chr11:66050105-66050126 chr11:66050116-66050125 chr11:66050111-66050127
24	POLR2A	chr11:66047062-66051216	HepG2	liver:	n/a	n/a
25	POLR2A	chr11:66048402-66051605	K562	blood:	n/a	n/a
26	POLR2A	chr11:66050793-66051013	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:66049761-66050961	GM12878	blood:	n/a	n/a
28	POLR2A	chr11:66050669-66051094	HepG2	liver:	n/a	n/a
29	MXI1	chr11:66049691-66051246	IMR90	lung:	n/a	chr11:66050008-66050023 chr11:66050006-66050021 chr11:66050049-66050064
30	POLR2A	chr11:66050547-66051189	GM12891	blood:	n/a	n/a
31	CTCF	chr11:66050800-66050950	AG10803	skin:	n/a	n/a
32	POLR2A	chr11:66049857-66051065	HepG2	liver:	n/a	n/a
33	POLR2A	chr11:66050701-66051072	GM12891	blood:	n/a	n/a
34	POLR2A	chr11:66050762-66051128	U87	brain:	n/a	n/a
35	POLR2A	chr11:66048813-66051508	HepG2	liver:	n/a	n/a
36	POLR2A	chr11:66049180-66052589	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66029401..66032337-chr11:66048852..66051047,2	MCF-7	breast:
2	chr11:66049888..66052811-chr11:66137402..66139383,3	MCF-7	breast:
3	chr11:65837641..65839546-chr11:66050688..66053288,2	K562	blood:
4	chr11:66050790..66053564-chr11:66079260..66081695,2	MCF-7	breast:
5	chr11:65624126..65626253-chr11:66048758..66051466,2	K562	blood:
6	chr11:66049515..66053153-chr11:66136549..66141980,4	K562	blood:

Variant related genes	Relation type
ENSG00000245156	TF binding region
ENSG00000172732	Chromatin interaction
ENSG00000254458	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000174669	Chromatin interaction
ENSG00000174996	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1151532	0.85[AFR][1000 genomes]
rs1190945	0.92[AFR][1000 genomes]
rs1190946	0.86[AFR][1000 genomes]
rs1191715	0.81[AFR][1000 genomes]
rs1203551	0.92[AFR][1000 genomes]
rs1203552	0.92[AFR][1000 genomes]
rs1203749	0.85[AFR][1000 genomes]
rs1203750	0.85[AFR][1000 genomes]
rs1203801	0.85[AFR][1000 genomes]
rs1630638	0.81[AFR][1000 genomes]
rs2452687	0.85[AFR][1000 genomes]
rs3017606	0.89[AFR][1000 genomes]
rs471709	0.82[AFR][1000 genomes]
rs472853	0.85[AFR][1000 genomes]
rs475817	0.85[AFR][1000 genomes]
rs477001	0.85[AFR][1000 genomes]
rs504456	0.85[AFR][1000 genomes]
rs505412	0.92[AFR][1000 genomes]
rs505642	0.85[AFR][1000 genomes]
rs510398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs512316	0.92[AFR][1000 genomes]
rs515778	0.92[AFR][1000 genomes]
rs519911	0.85[AFR][1000 genomes]
rs527279	0.85[AFR][1000 genomes]
rs547282	0.85[AFR][1000 genomes]
rs547892	0.85[AFR][1000 genomes]
rs549228	0.85[AFR][1000 genomes]
rs551652	0.85[AFR][1000 genomes]
rs555826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs560105	0.85[AFR][1000 genomes]
rs561199	0.85[AFR][1000 genomes]
rs561869	0.85[AFR][1000 genomes]
rs567414	0.85[AFR][1000 genomes]
rs568423	0.85[AFR][1000 genomes]
rs571368	0.92[AFR][1000 genomes]
rs572697	0.92[AFR][1000 genomes]
rs577301	0.85[AFR][1000 genomes]
rs581247	0.92[AFR][1000 genomes]
rs693382	0.85[AFR][1000 genomes]
rs7947668	0.81[AFR][1000 genomes]
rs948358	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs948477	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv897773	chr11:66041807-66063654	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv555223	chr11:66041807-66064126	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv897774	chr11:66042962-66063654	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv897775	chr11:66042962-66064850	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv897776	chr11:66042962-66066349	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv897777	chr11:66044882-66063654	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv897778	chr11:66044882-66066349	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv897779	chr11:66047523-66063654	Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66042000-66055600	Weak transcription	Fetal Kidney	kidney
2	chr11:66044200-66051800	Weak transcription	Fetal Lung	lung
3	chr11:66045600-66051800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr11:66045600-66051800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:66045600-66051800	Weak transcription	Esophagus	oesophagus
6	chr11:66045600-66052000	Weak transcription	Pancreas	Pancrea
7	chr11:66046000-66052200	Weak transcription	HMEC	breast
8	chr11:66046000-66054000	Weak transcription	Aorta	Aorta
9	chr11:66046600-66052800	Weak transcription	Right Atrium	heart
10	chr11:66046800-66051000	Enhancers	Fetal Thymus	thymus
11	chr11:66047200-66051600	Weak transcription	Lung	lung
12	chr11:66047400-66051000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:66047400-66052000	Weak transcription	NHEK	skin
14	chr11:66047400-66055400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:66047800-66051000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:66047800-66051200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
17	chr11:66047800-66053000	Enhancers	Fetal Brain Male	brain
18	chr11:66048200-66052000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:66048400-66051000	Enhancers	A549	lung
20	chr11:66048800-66051000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr11:66048800-66054200	Weak transcription	NH-A	brain
22	chr11:66049000-66051000	Genic enhancers	Fetal Stomach	stomach
23	chr11:66049000-66051200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:66049000-66051800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:66049000-66054400	Weak transcription	HSMM	muscle
26	chr11:66049200-66051000	Enhancers	Primary B cells from peripheral blood	blood
27	chr11:66049200-66051000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr11:66049200-66051000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:66049200-66051000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr11:66049400-66051000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr11:66049600-66051000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr11:66049600-66051000	Enhancers	Dnd41	blood
33	chr11:66049600-66051000	Enhancers	GM12878-XiMat	blood
34	chr11:66049800-66054800	Weak transcription	HSMMtube	muscle
35	chr11:66050000-66053600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:66050200-66051000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr11:66050200-66054800	Genic enhancers	Fetal Muscle Trunk	muscle
38	chr11:66050400-66051000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:66050400-66051000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:66050400-66051000	Genic enhancers	Thymus	Thymus
41	chr11:66050400-66051600	Weak transcription	Colonic Mucosa	Colon
42	chr11:66050400-66051600	Weak transcription	Ovary	ovary
43	chr11:66050400-66051800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:66050400-66052400	Weak transcription	Stomach Mucosa	stomach
45	chr11:66050400-66052600	Weak transcription	NHDF-Ad	bronchial
46	chr11:66050400-66053000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:66050400-66053600	Weak transcription	K562	blood
48	chr11:66050400-66054600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:66050400-66054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:66050400-66055000	Weak transcription	Left Ventricle	heart

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