Variant report

Variant	rs1503433
Chromosome Location	chr3:88037200-88037201
allele	G/T
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	EP300	chr3:88037089-88037354	K562	blood:	n/a	n/a
2	BACH1	chr3:88037114-88037548	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAFF	chr3:88037113-88037540	K562	blood:	n/a	n/a
4	POLR2A	chr3:88037176-88037286	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr3:88037133-88037448	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:88037080-88037851	K562	blood:	n/a	n/a
7	MAFK	chr3:88037111-88037448	K562	blood:	n/a	n/a
8	MAFK	chr3:88037176-88037376	HepG2	liver:	n/a	n/a
9	RCOR1	chr3:88037134-88037434	K562	blood:	n/a	n/a
10	MAFK	chr3:88037086-88037569	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
HTR1F	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10511136	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11128018	0.84[EUR][1000 genomes]
rs11128019	0.83[EUR][1000 genomes]
rs11717021	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11717413	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11915058	0.84[EUR][1000 genomes]
rs12714696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13074576	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431153	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469569	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1604699	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17025236	0.87[ASN][1000 genomes]
rs17025241	0.88[ASN][1000 genomes]
rs17549213	0.85[EUR][1000 genomes]
rs17549345	1.00[CEU][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs1835542	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1835543	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1946569	0.80[EUR][1000 genomes]
rs2016224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082226	0.83[ASN][1000 genomes]
rs2099229	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163423	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2344185	1.00[CEU][hapmap];0.81[CHD][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2880801	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2880802	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35040143	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858925	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858969	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858971	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858972	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858974	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858975	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55840331	0.85[EUR][1000 genomes]
rs56323967	0.83[ASN][1000 genomes]
rs58658187	0.88[ASN][1000 genomes]
rs60099577	0.84[EUR][1000 genomes]
rs67047416	0.84[EUR][1000 genomes]
rs67566069	0.88[ASN][1000 genomes]
rs6770013	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778211	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6781226	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781901	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785333	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6787253	0.88[ASN][1000 genomes]
rs6789002	0.81[EUR][1000 genomes]
rs6798161	0.87[ASN][1000 genomes]
rs68042814	0.84[EUR][1000 genomes]
rs6804848	0.88[ASN][1000 genomes]
rs68068970	0.87[ASN][1000 genomes]
rs73140133	0.88[ASN][1000 genomes]
rs73140134	0.86[ASN][1000 genomes]
rs7629565	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637503	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7652406	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310061	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9681975	0.88[ASN][1000 genomes]
rs9852704	1.00[CEU][hapmap];0.81[CHD][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9855839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859034	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9861809	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863076	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878862	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880480	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	esv3329288	chr3:88036062-88038010	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1503433	HTR1F	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88029600-88039800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:88030200-88045400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:88037000-88037400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:88037000-88037400	Enhancers	K562	blood
5	chr3:88037000-88037600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:88037000-88037600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:88037000-88037600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:88037000-88037600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:88037000-88037600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:88037000-88037800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:88037200-88037400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:88037200-88037600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:88037200-88037600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr3:88037200-88037600	Enhancers	A549	lung

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