Variant report

Variant	rs2041736
Chromosome Location	chr2:39890483-39890484
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	CTCF	chr2:39890460-39890610	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr2:39890420-39890570	WERI-Rb-1	eye:	n/a	n/a
3	CTCF	chr2:39890420-39890570	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr2:39890400-39890550	BE2_C	brain:	n/a	n/a
5	CTCF	chr2:39890460-39890610	GM12875	blood:	n/a	n/a
6	POLR2A	chr2:39890429-39890691	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr2:39890298-39890751	H1-neurons	neurons:	n/a	n/a
8	CTCF	chr2:39890400-39890550	HEK293	kidney:	n/a	n/a
9	CTCF	chr2:39890480-39890630	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr2:39890400-39890550	SK-N-SH_RA	brain:	n/a	n/a
11	ARID3A	chr2:39890418-39890572	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TMEM178A	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10170462	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10177801	0.87[EUR][1000 genomes]
rs10186346	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10208929	0.87[EUR][1000 genomes]
rs11124689	0.87[EUR][1000 genomes]
rs12613210	0.85[EUR][1000 genomes]
rs12712652	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12989245	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13384364	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13405084	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13409487	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1548870	0.87[EUR][1000 genomes]
rs1548871	0.87[EUR][1000 genomes]
rs1861244	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2058618	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2215956	0.87[EUR][1000 genomes]
rs2540200	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2540247	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2540248	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2540249	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2540250	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2540251	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2540252	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2540255	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2716682	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716683	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716684	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716686	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2716687	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2716688	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2716690	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2716691	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2716692	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2716693	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2716694	0.89[EUR][1000 genomes]
rs2716719	0.86[EUR][1000 genomes]
rs2716720	0.87[EUR][1000 genomes]
rs2716732	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2716737	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2716738	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35791480	0.84[EUR][1000 genomes]
rs4670952	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4670954	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6707177	0.85[EUR][1000 genomes]
rs6711206	0.81[EUR][1000 genomes]
rs6736442	0.87[EUR][1000 genomes]
rs6748628	0.86[EUR][1000 genomes]
rs917964	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs949812	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs949813	0.82[AMR][1000 genomes];0.96[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	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39885600-39893600	Weak transcription	Fetal Brain Male	brain
2	chr2:39888400-39892400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:39888600-39891200	Weak transcription	Fetal Brain Female	brain
4	chr2:39888600-39892000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:39888600-39892400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:39889400-39890800	Weak transcription	HSMM	muscle
7	chr2:39889400-39891000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:39889400-39891800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:39889800-39892200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:39890000-39892600	Weak transcription	HSMMtube	muscle
11	chr2:39890400-39890600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:39890400-39892400	Enhancers	Fetal Heart	heart

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