Variant report

Variant	rs2278939
Chromosome Location	chr4:186857890-186857891
allele	C/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	POLR2A	chr4:186857802-186858554	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr4:186857745-186858618	H1-neurons	neurons:	n/a	n/a
3	REST	chr4:186857792-186858570	H1-neurons	neurons:	n/a	n/a
4	REST	chr4:186857617-186858822	H1-neurons	neurons:	n/a	n/a
5	CTCF	chr4:186857880-186858030	HCPEpiC	choroid plexus:	n/a	n/a

Variant related genes	Relation type
SORBS2	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10002339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10002615	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10013071	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10021784	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10022762	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11733555	0.88[JPT][hapmap]
rs2034787	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs28532657	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28561493	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4862595	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs4862597	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4862598	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4862602	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6552935	0.89[JPT][hapmap]
rs6552938	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6833156	0.84[JPT][hapmap]
rs724072	0.89[JPT][hapmap]
rs7656292	0.89[JPT][hapmap]
rs7672034	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs7693781	0.82[CHD][hapmap];0.89[JPT][hapmap]

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	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1023917	chr4:186533075-186997806	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537420	chr4:186533075-186997806	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1015236	chr4:186696172-187004074	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022661	chr4:186789827-187122464	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv537422	chr4:186789827-187122464	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv1032178	chr4:186836629-186909596	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2278939	SORBS2	cis	parietal	SCAN
rs2278939	C4orf38	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:186847600-186864200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:186847800-186872400	Weak transcription	Right Atrium	heart
3	chr4:186853800-186858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:186857000-186858600	Enhancers	Fetal Brain Male	brain
5	chr4:186857200-186860200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:186857800-186858200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:186857800-186858200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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