Variant report

Variant	rs17500114
Chromosome Location	chr2:172896587-172896588
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172893225..172894892-chr2:172895220..172897617,2	MCF-7	breast:
2	chr2:172863330..172866297-chr2:172895128..172896991,2	K562	blood:
3	chr2:172895443..172898175-chr2:172947631..172951395,3	MCF-7	breast:
4	chr2:172889595..172892508-chr2:172896420..172898140,2	K562	blood:
5	chr2:172894437..172897042-chr2:172954737..172956688,2	MCF-7	breast:
6	chr2:172892888..172895304-chr2:172895689..172897604,2	K562	blood:
7	chr2:172896231..172898804-chr2:172903539..172906403,3	K562	blood:
8	chr2:172895941..172897535-chr2:172913713..172916052,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METAP1D-2	chr2:172896324-172897114	l_1987_chr2:172825346-172897114_testes

No data

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1008152	1.00[AMR][1000 genomes]
rs17428076	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]
rs17428174	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796058	1.00[MEX][hapmap]
rs55791993	0.90[AMR][1000 genomes]
rs55863868	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56218609	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62183804	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62183808	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62183809	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62183811	0.83[AMR][1000 genomes]
rs62183817	0.89[AMR][1000 genomes]
rs62183851	0.89[AMR][1000 genomes]
rs62183852	1.00[AMR][1000 genomes]
rs62183853	0.89[AMR][1000 genomes]
rs6704590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6737876	1.00[AMR][1000 genomes]
rs6749895	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6761111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72892835	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892859	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs788161	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs788164	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs788168	0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes]

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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17500114	SLC25A12	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
2	chr2:172878600-172898200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:172887200-172896600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:172887400-172902800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:172893200-172896600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:172893400-172896600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:172893600-172902000	Weak transcription	K562	blood
8	chr2:172894200-172896600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:172894400-172896600	Weak transcription	HepG2	liver
10	chr2:172895600-172897600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:172896000-172897200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:172896200-172897000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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