Variant report

Variant	rs349503
Chromosome Location	chr3:140229274-140229275
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	BCL11A	chr3:140229189-140229394	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr3:140229140-140229668	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr3:140229182-140229677	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:140229063-140229718	H1-neurons	neurons:	n/a	n/a
5	CEBPB	chr3:140229238-140229541	H1-hESC	embryonic stem cell:	n/a	chr3:140229394-140229407
6	SIN3A	chr3:140229092-140229758	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr3:140229072-140229623	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CLSTN2-AS1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12054019	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12488519	0.97[EUR][1000 genomes]
rs12494276	0.84[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs168387	0.88[CHD][hapmap]
rs16850356	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes]
rs16850427	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap]
rs180971	0.89[CHD][hapmap]
rs349508	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs349547	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs349565	0.86[CHD][hapmap]
rs349566	0.89[CHD][hapmap]
rs349567	0.89[CHD][hapmap]
rs349568	0.82[CHD][hapmap]
rs4683500	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs4683505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683506	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs495109	1.00[CEU][hapmap]
rs507760	0.84[EUR][1000 genomes]
rs536892	1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes]
rs544827	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566331	0.84[EUR][1000 genomes]
rs56684347	0.81[AFR][1000 genomes]
rs58159053	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6793607	0.97[LWK][hapmap];0.83[MKK][hapmap]
rs6806710	0.87[AFR][1000 genomes]
rs72632310	0.84[EUR][1000 genomes]
rs72632312	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72632313	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72992708	0.85[AFR][1000 genomes]
rs7433000	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9857310	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv591863	chr3:140126067-140274442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140224400-140247200	Weak transcription	Ovary	ovary
2	chr3:140225000-140236800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:140227400-140230000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:140227400-140230200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:140227400-140240800	Weak transcription	HSMMtube	muscle
6	chr3:140227800-140229800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:140227800-140229800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:140227800-140230000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:140228000-140229600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:140228000-140229800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:140228000-140230200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr3:140228200-140229600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:140228200-140229600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:140228200-140230000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:140228200-140230000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:140228400-140229400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:140228600-140230400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:140229000-140229400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:140229000-140230000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:140229200-140229400	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links