Variant report

Variant	rs17647012
Chromosome Location	chr1:216249076-216249077
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	GATA2	chr1:216248855-216249174	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr1:216249010-216249148	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000233620	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11120734	1.00[CHB][hapmap]
rs11120735	1.00[CHB][hapmap]
rs1830857	1.00[MKK][hapmap]
rs2926178	1.00[CHD][hapmap]
rs301732	0.85[ASN][1000 genomes]
rs41303063	1.00[ASN][1000 genomes]
rs421821	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs440921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs446247	1.00[MKK][hapmap]
rs452747	1.00[MKK][hapmap]
rs503092	0.85[ASN][1000 genomes]
rs56219666	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56222536	1.00[ASN][1000 genomes]
rs682319	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv428599	chr1:216086224-216267211	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv873172	chr1:216144827-216281673	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216244400-216250800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:216246200-216249400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:216247400-216249200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr1:216247600-216249200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:216247800-216249200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:216248000-216249600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:216248400-216249400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:216248400-216250400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:216248600-216249200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr1:216248600-216249200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:216248600-216249200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:216248600-216249200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:216248600-216249200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:216248600-216249200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr1:216248600-216249200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:216248600-216249200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:216248600-216249200	Enhancers	HSMM	muscle
18	chr1:216248600-216249400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:216248600-216249400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:216248600-216249400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:216249000-216250000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:216249000-216260200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links