Variant report

Variant	rs12058480
Chromosome Location	chr1:155100845-155100846
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	MAZ	chr1:155098626-155101411	IMR90	lung:	n/a	chr1:155098727-155098736 chr1:155100204-155100214 chr1:155098728-155098735 chr1:155098726-155098736 chr1:155098725-155098740 chr1:155098726-155098737 chr1:155101097-155101113
2	SIN3AK20	chr1:155097963-155100883	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:155098341-155102845	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:155096985-155102845	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:155098247-155101166	Hela-S3	cervix:	n/a	n/a
6	TFAP2C	chr1:155096588-155102821	Hela-S3	cervix:	n/a	chr1:155098584-155098599 chr1:155102536-155102551 chr1:155100255-155100270
7	POLR2A	chr1:155100236-155102479	HepG2	liver:	n/a	n/a
8	SIN3AK20	chr1:155100744-155101124	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr1:155097222-155104778	HepG2	liver:	n/a	n/a
10	TCF12	chr1:155098540-155101015	A549	lung:	n/a	chr1:155098891-155098901 chr1:155099951-155099958 chr1:155099218-155099227 chr1:155098553-155098560
11	POLR2A	chr1:155099456-155102550	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:155100249-155104737	HepG2	liver:	n/a	n/a
13	ZBTB7A	chr1:155099557-155102902	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr1:155100694-155100935	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:155098856-155101269	SK-N-MC	brain:	n/a	n/a
16	SMARCB1	chr1:155098380-155100968	Hela-S3	cervix:	n/a	n/a
17	HEY1	chr1:155096801-155104706	HepG2	liver:	n/a	n/a
18	HDAC2	chr1:155098098-155100912	MCF-7	breast:	n/a	chr1:155100759-155100773
19	POLR2A	chr1:155099268-155102650	HUVEC	blood vessel:	n/a	n/a
20	MXI1	chr1:155099180-155103687	SK-N-SH	brain:	n/a	n/a
21	TFAP2A	chr1:155096837-155100905	Hela-S3	cervix:	n/a	chr1:155100333-155100348 chr1:155097090-155097101 chr1:155097714-155097726 chr1:155100258-155100269 chr1:155098586-155098596 chr1:155097090-155097101 chr1:155097086-155097101 chr1:155100714-155100722 chr1:155097193-155097204 chr1:155098586-155098596 chr1:155098586-155098596 chr1:155097193-155097204 chr1:155100258-155100269 chr1:155100258-155100269 chr1:155100258-155100269 chr1:155097193-155097204 chr1:155098584-155098598 chr1:155097714-155097725 chr1:155100714-155100722 chr1:155098600-155098608 chr1:155100714-155100722 chr1:155097090-155097101 chr1:155099311-155099323 chr1:155097193-155097204 chr1:155098586-155098598 chr1:155098586-155098596 chr1:155097090-155097101
22	ZNF263	chr1:155100404-155100877	HEK293-T-REx	kidney:	n/a	chr1:155100671-155100692
23	POLR2A	chr1:155100102-155100866	MCF-7	breast:	n/a	n/a
24	POLR2A	chr1:155097219-155102660	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:155097075-155102743	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr1:155096996-155102672	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:155099788-155100916	K562	blood:	n/a	n/a
28	MAX	chr1:155096829-155101044	HepG2	liver:	n/a	chr1:155098727-155098736 chr1:155100204-155100214 chr1:155098442-155098451 chr1:155098728-155098735 chr1:155098441-155098451 chr1:155098442-155098451 chr1:155098726-155098736 chr1:155098441-155098452 chr1:155098725-155098740 chr1:155098442-155098451 chr1:155098441-155098452 chr1:155098726-155098737 chr1:155098440-155098455
29	MAX	chr1:155097880-155101068	MCF-7	breast:	n/a	chr1:155098727-155098736 chr1:155100204-155100214 chr1:155098442-155098451 chr1:155098728-155098735 chr1:155098441-155098451 chr1:155098442-155098451 chr1:155098726-155098736 chr1:155098441-155098452 chr1:155098725-155098740 chr1:155098442-155098451 chr1:155098441-155098452 chr1:155098726-155098737 chr1:155098440-155098455
30	HEY1	chr1:155097245-155102620	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:155100252-155104734	HepG2	liver:	n/a	n/a
32	CREB1	chr1:155096857-155101194	HepG2	liver:	n/a	chr1:155098014-155098027
33	POLR2A	chr1:155098646-155104670	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155099451..155102336-chr6:27776687..27779634,2	MCF-7	breast:
2	chr1:154986410..154988338-chr1:155099789..155102344,2	MCF-7	breast:
3	chr1:154973069..154975738-chr1:155098828..155103753,6	MCF-7	breast:
4	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
5	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
6	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
7	chr1:154971203..154978007-chr1:155093683..155103687,24	MCF-7	breast:
8	chr1:155099426..155102245-chr1:155118836..155121124,2	K562	blood:
9	chr1:154942779..154946822-chr1:155099948..155103477,6	MCF-7	breast:
10	chr1:155096309..155104200-chr1:155157595..155166389,23	MCF-7	breast:
11	chr1:154190385..154194245-chr1:155097625..155102022,4	MCF-7	breast:
12	chr1:155098824..155101489-chr1:155162030..155163615,2	K562	blood:
13	chr1:155099597..155102197-chr20:52823453..52826190,2	MCF-7	breast:
14	chr1:155098008..155101008-chr1:155194682..155198746,4	MCF-7	breast:
15	chr1:155033872..155036303-chr1:155100815..155102776,3	MCF-7	breast:
16	chr1:154927921..154930656-chr1:155100547..155102182,2	MCF-7	breast:
17	chr1:155099520..155102330-chr1:155176910..155178560,2	K562	blood:
18	chr1:154909403..154911372-chr1:155099659..155102635,3	MCF-7	breast:
19	chr1:155022054..155026411-chr1:155097710..155103379,8	MCF-7	breast:

Variant related genes	Relation type
EFNA1	TF binding region
ENSG00000163344	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000273088	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000173171	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000223452	Chromatin interaction
ENSG00000163346	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11465207	1.00[CHB][hapmap]
rs12061020	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12748855	1.00[CEU][hapmap]
rs12760148	1.00[CHB][hapmap]
rs1611772	1.00[CHB][hapmap]
rs4845402	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers 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
4	nsv998756	chr1:155080090-155136545	Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
6	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
7	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
8	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
9	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155098400-155101200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:155098400-155101200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:155098400-155101600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr1:155098400-155101800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
5	chr1:155098400-155103200	Active TSS	Liver	Liver
6	chr1:155098600-155101200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
7	chr1:155098600-155101600	Active TSS	Brain Angular Gyrus	brain
8	chr1:155098600-155101600	Active TSS	Brain Anterior Caudate	brain
9	chr1:155098600-155101600	Active TSS	Brain Substantia Nigra	brain
10	chr1:155098800-155101400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:155098800-155101400	Active TSS	Right Atrium	heart
12	chr1:155098800-155102000	Active TSS	Psoas Muscle	Psoas
13	chr1:155098800-155103000	Active TSS	Gastric	stomach
14	chr1:155098800-155103400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:155099000-155101000	Bivalent/Poised TSS	Fetal Kidney	kidney
16	chr1:155099000-155101800	Active TSS	Brain Cingulate Gyrus	brain
17	chr1:155099000-155102000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr1:155099200-155101400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
19	chr1:155099200-155101800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:155099200-155102800	Bivalent/Poised TSS	HepG2	liver
21	chr1:155099200-155103200	Active TSS	Small Intestine	intestine
22	chr1:155099400-155101000	Active TSS	Ovary	ovary
23	chr1:155099400-155101200	Flanking Bivalent TSS/Enh	Dnd41	blood
24	chr1:155099400-155101400	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr1:155099400-155102000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:155099600-155102200	Active TSS	Brain Hippocampus Middle	brain
27	chr1:155099600-155103600	Active TSS	Left Ventricle	heart
28	chr1:155099800-155101000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:155099800-155101000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:155099800-155101400	Active TSS	A549	lung
31	chr1:155099800-155101600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:155099800-155101600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
33	chr1:155099800-155102800	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:155099800-155103600	Active TSS	Lung	lung
35	chr1:155100000-155101000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:155100000-155101000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr1:155100000-155103400	Active TSS	Esophagus	oesophagus
38	chr1:155100200-155101400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:155100200-155101400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:155100200-155101400	Active TSS	Pancreas	Pancrea
41	chr1:155100200-155101600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:155100200-155102000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:155100200-155102200	Active TSS	Stomach Mucosa	stomach
44	chr1:155100400-155101000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:155100400-155101000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:155100400-155101000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:155100400-155101000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:155100400-155101000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:155100400-155101000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:155100400-155101000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell

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