Variant report

Variant	rs12133583
Chromosome Location	chr1:113240790-113240791
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113240662-113240807	A549	lung:	n/a	n/a
2	POLR2A	chr1:113240102-113248907	U87	brain:	n/a	n/a
3	POLR2A	chr1:113240789-113240796	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:113240693-113241711	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:113240738-113245862	K562	blood:	n/a	n/a
6	POLR2A	chr1:113240207-113248892	K562	blood:	n/a	n/a
7	POLR2A	chr1:113240458-113241069	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:113240680-113249021	K562	blood:	n/a	n/a
9	POLR2A	chr1:113240452-113240879	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr1:113240211-113248533	A549	lung:	n/a	n/a
11	POLR2A	chr1:113240649-113246839	K562	blood:	n/a	n/a
12	POLR2A	chr1:113240403-113244696	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr1:113240166-113244996	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr1:113240656-113240801	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:113240732-113241475	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:113240375-113248999	K562	blood:	n/a	n/a
17	POLR2A	chr1:113240720-113241982	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr1:113240783-113246836	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr1:113240610-113244540	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:113240176-113246017	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:113240249-113248607	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:113240688-113241670	IMR90	lung:	n/a	n/a
23	POLR2A	chr1:113240102-113248913	U87	brain:	n/a	n/a
24	POLR2A	chr1:113240145-113241880	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
3	chr1:113160176..113163931-chr1:113238020..113242018,6	K562	blood:
4	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
5	chr1:112937855..112940278-chr1:113239914..113242532,2	MCF-7	breast:
6	chr1:113240296..113243095-chr1:113496225..113498995,2	K562	blood:
7	chr1:113215224..113219998-chr1:113238829..113244717,20	MCF-7	breast:
8	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
9	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

No data

Variant related genes	Relation type
MOV10	TF binding region
ENSG00000225075	TF binding region
ENSG00000155380	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000271810	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1106287	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110042	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102513	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11102514	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11102520	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12030612	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12030641	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12040988	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12120956	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12122980	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12126684	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12126971	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12130243	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12406282	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728311	0.84[EUR][1000 genomes]
rs12756815	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17030613	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17030651	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2009056	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2279499	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2306937	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2306940	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887882	0.87[EUR][1000 genomes]
rs34848593	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748656	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795819	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61818802	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61818805	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883593	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308256	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]

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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv997362	chr1:113234820-113243297	Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12133583	ST7L	cis	multi-tissue	Pritchard
rs12133583	ST7L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113218600-113240800	Weak transcription	Right Atrium	heart
2	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
3	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
4	chr1:113222000-113243000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:113228600-113242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:113228600-113242800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:113229000-113242200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:113229600-113243200	Strong transcription	Dnd41	blood
10	chr1:113230200-113240800	Strong transcription	Adipose Nuclei	Adipose
11	chr1:113230200-113241200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:113230200-113242600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:113230200-113243000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:113230200-113243200	Strong transcription	Primary T cells from cord blood	blood
15	chr1:113230400-113241200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:113230600-113240800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:113230600-113241000	Strong transcription	Gastric	stomach
18	chr1:113230600-113241400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:113230600-113242200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:113230600-113242600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr1:113230800-113241400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:113231200-113241400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:113231400-113241800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:113231600-113241200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:113231600-113243000	Weak transcription	Psoas Muscle	Psoas
28	chr1:113231600-113243200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:113231800-113242400	Strong transcription	Osteobl	bone
30	chr1:113231800-113242600	Strong transcription	Fetal Lung	lung
31	chr1:113232000-113241000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:113232000-113241000	Strong transcription	Hela-S3	cervix
33	chr1:113232000-113241400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:113232000-113242400	Strong transcription	Fetal Stomach	stomach
35	chr1:113232000-113242600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:113232200-113241000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:113232200-113241400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:113232200-113241800	Strong transcription	Colon Smooth Muscle	Colon
39	chr1:113232200-113241800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:113232400-113242000	Strong transcription	Brain Hippocampus Middle	brain
41	chr1:113232400-113242600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:113232600-113241200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:113232800-113240800	Strong transcription	Fetal Thymus	thymus
44	chr1:113233000-113242200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:113233200-113241000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:113234000-113240800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:113234000-113240800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:113234000-113241200	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:113234000-113241600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:113234000-113242800	Strong transcription	Brain Anterior Caudate	brain

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