Variant report

Variant	rs12759003
Chromosome Location	chr1:192602436-192602437
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	GATA3	chr1:192601409-192602480	SK-N-SH	brain:	n/a	chr1:192601667-192601688 chr1:192601501-192601508 chr1:192601669-192601685
2	GATA2	chr1:192601366-192602465	SH-SY5Y	brain:	n/a	chr1:192601667-192601688 chr1:192601501-192601508 chr1:192601669-192601685
3	EP300	chr1:192601024-192602965	SK-N-SH	brain:	n/a	chr1:192602878-192602892
4	EP300	chr1:192601392-192602442	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:192601062..192603438-chr1:192604359..192606960,2	K562	blood:

Variant related genes	Relation type
RGS13	TF binding region
ENSG00000127074	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10127997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044559	0.98[EUR][1000 genomes]
rs3795617	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3884536	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233424	0.98[EUR][1000 genomes]
rs4319308	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59105666	0.98[EUR][1000 genomes]
rs7553821	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv467005	chr1:192549912-192625360	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv548659	chr1:192549912-192625360	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192597000-192605600	Enhancers	Fetal Lung	lung
2	chr1:192597800-192602600	Enhancers	Liver	Liver
3	chr1:192598800-192603200	Weak transcription	Right Ventricle	heart
4	chr1:192599000-192608200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:192600200-192620400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:192601400-192602800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:192601400-192603200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:192601600-192602600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:192601600-192603000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr1:192601600-192603200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:192601600-192604000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:192601600-192607000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:192601800-192602600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:192601800-192602800	Enhancers	Fetal Intestine Large	intestine
15	chr1:192601800-192603200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:192601800-192604400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:192602000-192602600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:192602000-192602800	Enhancers	HepG2	liver
19	chr1:192602000-192604000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:192602200-192602600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:192602400-192602600	Enhancers	HSMMtube	muscle
22	chr1:192602400-192602800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:192602400-192602800	Weak transcription	Fetal Heart	heart
24	chr1:192602400-192603000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:192602400-192603200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:192602400-192603200	Enhancers	Psoas Muscle	Psoas
27	chr1:192602400-192603200	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links