Variant report

Variant	rs2307117
Chromosome Location	chr5:57787376-57787377
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	SPI1	chr5:57787026-57787417	HL-60	blood:	n/a	chr5:57787284-57787297 chr5:57787203-57787210
2	SPI1	chr5:57786992-57787450	HL-60	blood:	n/a	chr5:57787284-57787297 chr5:57787203-57787210
3	MYC	chr5:57787022-57787535	NB4	blood:	n/a	n/a
4	SPI1	chr5:57787107-57787389	GM12878	blood:	n/a	chr5:57787284-57787297 chr5:57787203-57787210
5	MAX	chr5:57787082-57787569	NB4	blood:	n/a	n/a

Variant related genes	Relation type
GAPT	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10035587	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10056043	0.98[ASN][1000 genomes]
rs10071540	0.98[ASN][1000 genomes]
rs10071783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10074748	0.95[ASN][1000 genomes]
rs10472062	0.94[ASN][1000 genomes]
rs11745321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11955212	0.90[ASN][1000 genomes]
rs12173136	0.95[ASN][1000 genomes]
rs12187683	0.90[ASN][1000 genomes]
rs1422230	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1605741	0.87[CHB][hapmap]
rs1605742	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs17712820	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs4551014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700297	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57211722	0.86[ASN][1000 genomes]
rs57367646	0.93[ASN][1000 genomes]
rs6865094	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6869174	0.98[ASN][1000 genomes]
rs6870990	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6890117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6890154	1.00[ASN][1000 genomes]
rs6890362	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6890847	0.82[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6891534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6895777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6895889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6896790	0.87[CHB][hapmap]
rs73094379	0.90[ASN][1000 genomes]
rs7712288	0.87[ASN][1000 genomes]
rs7723416	0.87[CHB][hapmap];0.81[CHD][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2307117	GAPT	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57785800-57787600	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr5:57785800-57787600	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr5:57785800-57787800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:57786000-57787400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr5:57786000-57787800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:57786200-57787600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr5:57786200-57788200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:57786800-57795800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:57787000-57787400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:57787000-57787600	Active TSS	Primary hematopoietic stem cells	blood
11	chr5:57787000-57788000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:57787200-57787400	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr5:57787200-57787400	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr5:57787200-57787600	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:57787200-57787800	Active TSS	Primary B cells from cord blood	blood
16	chr5:57787200-57788200	Active TSS	Monocytes-CD14+_RO01746	blood
17	chr5:57787200-57788400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr5:57787200-57788600	Active TSS	Primary monocytes fromperipheralblood	blood
19	chr5:57787200-57789000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:57787200-57789400	Active TSS	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links