Variant report

Variant	rs12135970
Chromosome Location	chr1:156338518-156338519
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	MYBL2	chr1:156338493-156339193	HepG2	liver:	n/a	n/a
2	FOXA1	chr1:156337949-156338538	HepG2	liver:	n/a	n/a
3	GATA3	chr1:156337878-156338589	SK-N-SH	brain:	n/a	chr1:156338223-156338240
4	POLR2A	chr1:156336907-156344214	HepG2	liver:	n/a	n/a
5	GATA3	chr1:156337649-156338574	SK-N-SH	brain:	n/a	chr1:156338223-156338240
6	GATA3	chr1:156337793-156338531	MCF-7	breast:	n/a	chr1:156338223-156338240
7	ZEB1	chr1:156336577-156339970	HepG2	liver:	n/a	chr1:156338920-156338927
8	GATA3	chr1:156337775-156338571	MCF-7	breast:	n/a	chr1:156338223-156338240

No.	Distal block	Cell Line	Cell type
1	chr1:156337757..156339382-chr1:156424916..156426755,2	MCF-7	breast:
2	chr1:156335306..156343282-chr1:156347773..156352892,8	MCF-7	breast:
3	chr1:156304937..156307794-chr1:156336669..156339422,4	MCF-7	breast:
4	chr1:156305358..156309501-chr1:156336177..156340436,7	MCF-7	breast:

Variant related genes	Relation type
CCT3	TF binding region
RHBG	TF binding region
ENSG00000236947	Chromatin interaction
ENSG00000132677	Chromatin interaction
ENSG00000163467	Chromatin interaction
ENSG00000163468	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11264478	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264479	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129175	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12131479	0.96[ASN][1000 genomes]
rs12141630	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv915822	chr1:156226286-156651655	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases
4	nsv872471	chr1:156287360-156356480	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv470742	chr1:156335111-156354367	Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156335800-156338600	Weak transcription	Esophagus	oesophagus
2	chr1:156335800-156338600	Enhancers	Fetal Intestine Small	intestine
3	chr1:156336400-156339000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:156336800-156339200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:156337000-156338800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:156337200-156339000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:156337400-156338600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:156337600-156339000	Enhancers	Fetal Lung	lung
9	chr1:156337800-156338800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr1:156337800-156339000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:156337800-156339000	Active TSS	HepG2	liver
12	chr1:156338000-156338600	Enhancers	Pancreas	Pancrea
13	chr1:156338000-156338800	Bivalent Enhancer	Fetal Stomach	stomach
14	chr1:156338000-156339000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:156338000-156339000	Bivalent Enhancer	Placenta	Placenta
16	chr1:156338200-156338600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:156338200-156338600	Enhancers	Liver	Liver
18	chr1:156338200-156338600	Enhancers	A549	lung
19	chr1:156338200-156338800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:156338200-156338800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:156338200-156339000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:156338200-156339000	Weak transcription	K562	blood
23	chr1:156338200-156341400	Weak transcription	Hela-S3	cervix
24	chr1:156338400-156338600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:156338400-156338600	Bivalent Enhancer	Fetal Intestine Large	intestine
26	chr1:156338400-156338600	Enhancers	Ovary	ovary
27	chr1:156338400-156338800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:156338400-156338800	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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