Variant report

Variant	rs3749056
Chromosome Location	chr2:40484945-40484946
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	REST	chr2:40484895-40485751	H1-neurons	neurons:	n/a	chr2:40485356-40485365
2	TCF7L2	chr2:40484899-40485253	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:40484878-40485674	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr2:40484836-40485679	H1-neurons	neurons:	n/a	n/a
5	GATA2	chr2:40484574-40485170	SH-SY5Y	brain:	n/a	chr2:40484706-40484713 chr2:40484963-40484975 chr2:40485091-40485101
6	REST	chr2:40484521-40485813	H1-neurons	neurons:	n/a	chr2:40485356-40485365

Variant related genes	Relation type
ENSG00000268898	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs105288	1.00[JPT][hapmap]
rs1641458	1.00[JPT][hapmap]
rs34971853	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36184451	0.88[ASN][1000 genomes]
rs366578	1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs368642	1.00[JPT][hapmap]
rs369140	1.00[JPT][hapmap]
rs371909	0.87[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs372052	1.00[JPT][hapmap]
rs373606	0.90[JPT][hapmap]
rs379410	1.00[JPT][hapmap]
rs380082	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.95[ASN][1000 genomes]
rs380975	1.00[JPT][hapmap]
rs384511	1.00[JPT][hapmap]
rs384994	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs385561	1.00[JPT][hapmap]
rs389109	1.00[JPT][hapmap]
rs389992	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs391631	1.00[JPT][hapmap]
rs391984	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs393711	1.00[JPT][hapmap]
rs394112	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[ASN][1000 genomes]
rs394540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs398175	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs399061	1.00[JPT][hapmap]
rs401815	1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs402307	1.00[JPT][hapmap]
rs403630	0.83[GIH][hapmap]
rs405884	1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs406222	1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs406880	1.00[JPT][hapmap]
rs407267	1.00[JPT][hapmap]
rs407388	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[ASN][1000 genomes]
rs407889	1.00[JPT][hapmap]
rs408009	1.00[JPT][hapmap]
rs413711	1.00[JPT][hapmap]
rs415695	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs417464	1.00[JPT][hapmap]
rs417591	1.00[JPT][hapmap]
rs417873	1.00[JPT][hapmap]
rs418780	0.90[JPT][hapmap]
rs421870	1.00[JPT][hapmap]
rs426295	1.00[JPT][hapmap]
rs427632	1.00[JPT][hapmap]
rs428738	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs430314	1.00[JPT][hapmap]
rs432769	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs434082	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];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs436010	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs439960	1.00[JPT][hapmap]
rs440155	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs441196	1.00[JPT][hapmap]
rs441413	0.90[JPT][hapmap]
rs441593	1.00[JPT][hapmap]
rs442586	1.00[JPT][hapmap]
rs443236	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs450116	1.00[JPT][hapmap]
rs450823	1.00[JPT][hapmap]
rs451074	0.81[JPT][hapmap]
rs451158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs451811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs452138	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs505473	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs581477	1.00[JPT][hapmap]
rs581568	1.00[JPT][hapmap]
rs615449	0.87[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs666362	0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs674128	0.93[ASN][1000 genomes]
rs678107	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs679339	1.00[JPT][hapmap]
rs688673	1.00[JPT][hapmap]
rs72794789	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873912	chr2:40468418-40492315	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873913	chr2:40469705-40485074	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
QRS duration in Tripanosoma cruzi seropositivity	24324551	GWAS catalog

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40451400-40490000	Weak transcription	Dnd41	blood
3	chr2:40467800-40487400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:40472600-40487200	Weak transcription	HSMM	muscle
5	chr2:40475800-40485400	Weak transcription	Right Atrium	heart
6	chr2:40478600-40487000	Weak transcription	Hela-S3	cervix
7	chr2:40478800-40496600	Weak transcription	Right Ventricle	heart
8	chr2:40478800-40499600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:40479000-40487400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:40479400-40488000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:40479800-40485000	Weak transcription	Left Ventricle	heart
12	chr2:40481200-40485200	Enhancers	Brain Germinal Matrix	brain
13	chr2:40482400-40490200	Weak transcription	Aorta	Aorta
14	chr2:40483200-40485000	Weak transcription	Fetal Brain Male	brain
15	chr2:40483200-40490200	Enhancers	Fetal Heart	heart

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