Variant report

Variant	rs12133294
Chromosome Location	chr1:45988764-45988765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr1:45986470-45988984	A549	lung:	n/a	n/a
2	RFX5	chr1:45986992-45988879	Hela-S3	cervix:	n/a	chr1:45987244-45987253
3	GATA3	chr1:45987074-45988775	A549	lung:	n/a	n/a
4	MAX	chr1:45986698-45989010	A549	lung:	n/a	chr1:45987231-45987241 chr1:45987230-45987241 chr1:45987231-45987241 chr1:45987231-45987240 chr1:45987232-45987239 chr1:45987227-45987242 chr1:45987230-45987241 chr1:45987230-45987240 chr1:45987231-45987240
5	SP1	chr1:45986694-45988854	A549	lung:	n/a	chr1:45987640-45987651 chr1:45987628-45987639
6	POLR2A	chr1:45986694-45988775	Hela-S3	cervix:	n/a	n/a
7	EP300	chr1:45987127-45988814	A549	lung:	n/a	n/a
8	POLR2A	chr1:45986970-45988826	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:45986326-45988774	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:45988407-45988773	H1-hESC	embryonic stem cell:	n/a	n/a
11	KAP1	chr1:45987294-45988866	U2OS	brain:	n/a	n/a
12	POLR2A	chr1:45986011-45988798	HepG2	liver:	n/a	n/a
13	SP1	chr1:45987173-45988880	A549	lung:	n/a	chr1:45987640-45987651 chr1:45987628-45987639
14	POLR2A	chr1:45986415-45988822	HCT-116	colon:	n/a	n/a
15	NR2F2	chr1:45986441-45988931	K562	blood:	n/a	n/a
16	POLR2A	chr1:45986300-45988797	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45984510..45988941-chr1:46031540..46035902,8	MCF-7	breast:
2	chr1:45973182..45975128-chr1:45984664..45989019,3	MCF-7	breast:
3	chr1:45184712..45189957-chr1:45986029..45989344,7	K562	blood:
4	chr1:45985920..45989261-chr1:46150872..46154561,4	K562	blood:
5	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
6	chr1:45186094..45189073-chr1:45986029..45988855,6	K562	blood:
7	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
8	chr1:45954972..45958180-chr1:45986651..45988959,5	K562	blood:
9	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
10	chr1:45805140..45807328-chr1:45987853..45992059,3	K562	blood:
11	chr1:45984465..45989261-chr1:46150683..46156386,7	K562	blood:
12	chr1:45988000..45988805-chr6:30688919..30689665,2	Hela-S3	cervix:
13	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
14	chr1:45982844..45990993-chr1:46030121..46038313,25	K562	blood:
15	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
16	chr1:45284090..45287076-chr1:45986937..45989870,4	K562	blood:
17	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
18	chr1:45986151..45989227-chr1:46047437..46050636,3	MCF-7	breast:
19	chr1:45476953..45479637-chr1:45985604..45989189,5	K562	blood:
20	chr1:45239811..45242258-chr1:45985710..45988896,3	K562	blood:
21	chr1:45986916..45989039-chr1:46073191..46077083,3	K562	blood:
22	chr1:45987332..45989335-chr1:46087766..46089426,2	K562	blood:
23	chr1:45985342..45989391-chr1:46011113..46019467,18	MCF-7	breast:
24	chr1:45985980..45988948-chr1:46213742..46217743,4	K562	blood:
25	chr1:45982735..45988890-chr1:46031987..46038228,10	MCF-7	breast:
26	chr1:45195127..45198642-chr1:45986086..45989017,4	K562	blood:

No data

Variant related genes	Relation type
PRDX1	TF binding region
ENSG00000159588	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000197429	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10789465	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890331	0.81[AMR][1000 genomes]
rs11211122	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211130	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211135	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211136	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11580609	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11582118	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11802397	0.80[EUR][1000 genomes]
rs12119202	0.80[AMR][1000 genomes]
rs12568144	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12729715	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12743512	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2275276	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2356413	0.81[AMR][1000 genomes]
rs2356551	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2356553	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2453404	0.82[EUR][1000 genomes]
rs2934856	0.84[EUR][1000 genomes]
rs2934859	0.84[EUR][1000 genomes]
rs2991970	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2991971	0.83[EUR][1000 genomes]
rs2991972	0.84[EUR][1000 genomes]
rs2991973	0.83[EUR][1000 genomes]
rs2991974	0.83[EUR][1000 genomes]
rs2993262	0.84[EUR][1000 genomes]
rs35092140	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660861	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4660869	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660876	0.84[EUR][1000 genomes]
rs512026	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs518365	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs523526	0.84[EUR][1000 genomes]
rs60608374	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs606542	0.83[EUR][1000 genomes]
rs622798	0.84[EUR][1000 genomes]
rs644915	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6661321	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs666720	0.83[EUR][1000 genomes]
rs667626	0.84[EUR][1000 genomes]
rs7526571	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7526665	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs781058	0.81[AMR][1000 genomes]
rs7903	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9147	0.84[EUR][1000 genomes]
rs937291	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9429079	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs945180	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998199	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS 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 target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12133294	CCDC163P	cis	Nerve Tibial	GTEx
rs12133294	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs12133294	CCDC163P	cis	Artery Aorta	GTEx
rs12133294	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs12133294	CCDC163P	cis	Thyroid	GTEx
rs12133294	CCDC163P	cis	Esophagus Muscularis	GTEx
rs12133294	CCDC163P	cis	lung	GTEx
rs12133294	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs12133294	CCDC163P	cis	Esophagus Mucosa	GTEx
rs12133294	CCDC163P	cis	Muscle Skeletal	GTEx
rs12133294	GPBP1L1	cis	Whole Blood	GTEx
rs12133294	CCDC163P	cis	Heart Left Ventricle	GTEx
rs12133294	CCDC163P	cis	Stomach	GTEx
rs12133294	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs12133294	CCDC163P	cis	Artery Tibial	GTEx
rs12133294	CCDC163P	cis	Whole Blood	GTEx
rs12133294	MUTYH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45985400-45988800	Active TSS	A549	lung
2	chr1:45986600-45988800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:45987800-45988800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:45987800-45988800	Flanking Active TSS	HepG2	liver
5	chr1:45987800-45988800	Flanking Active TSS	K562	blood
6	chr1:45987800-45989000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:45987800-45989000	Flanking Active TSS	NHEK	skin
8	chr1:45988200-45988800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:45988200-45988800	Active TSS	Brain Angular Gyrus	brain
10	chr1:45988200-45989000	Enhancers	Placenta	Placenta
11	chr1:45988200-45989200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:45988200-45989200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:45988200-45989200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:45988200-45990000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:45988200-45990000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:45988200-45990600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:45988200-45990600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:45988200-45990800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:45988200-45990800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:45988200-45991000	Enhancers	Dnd41	blood
21	chr1:45988200-45992200	Weak transcription	Fetal Lung	lung
22	chr1:45988200-45993000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:45988400-45988800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:45988400-45988800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:45988400-45988800	Active TSS	Adipose Nuclei	Adipose
26	chr1:45988400-45988800	Enhancers	NH-A	brain
27	chr1:45988400-45988800	Enhancers	NHDF-Ad	bronchial
28	chr1:45988400-45989000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:45988400-45989000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:45988400-45989000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:45988400-45989200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:45988400-45989400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:45988400-45990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:45988400-45992200	Weak transcription	Fetal Intestine Large	intestine
35	chr1:45988400-45992200	Weak transcription	Fetal Kidney	kidney
36	chr1:45988400-45993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:45988400-45997200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:45988600-45988800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:45988600-45988800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:45988600-45989000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:45988600-45989000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:45988600-45989000	Enhancers	Stomach Mucosa	stomach
43	chr1:45988600-45989200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:45988600-45989200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:45988600-45989200	Flanking Active TSS	Hela-S3	cervix
46	chr1:45988600-45990000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr1:45988600-45990600	Weak transcription	HSMMtube	muscle
48	chr1:45988600-45991000	Weak transcription	Liver	Liver
49	chr1:45988600-45992200	Weak transcription	Fetal Heart	heart
50	chr1:45988600-45992200	Weak transcription	Fetal Intestine Small	intestine

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