Variant report

Variant	rs262012
Chromosome Location	chr5:177982013-177982014
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs171889	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs185493	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs262007	0.91[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs262010	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262017	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs262045	0.83[MEX][hapmap]
rs262053	0.86[ASN][1000 genomes]
rs262062	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs262066	0.81[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs262071	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4976794	0.83[EUR][1000 genomes]
rs566974	0.94[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv462570	chr5:177860454-178010145	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv600423	chr5:177860454-178010145	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs262012	LOC202181	cis	cerebellum	SCAN
rs262012	DOK3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177974400-177986200	Weak transcription	Right Atrium	heart
2	chr5:177974600-177982400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:177975400-177982400	Weak transcription	Right Ventricle	heart
4	chr5:177979400-177982400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:177981400-177983400	Enhancers	K562	blood
6	chr5:177981600-177982800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr5:177981600-177983400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:177981600-177985200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:177981800-177982400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
10	chr5:177981800-177982400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr5:177982000-177982200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:177982000-177982200	Enhancers	Stomach Smooth Muscle	stomach
13	chr5:177982000-177982400	Enhancers	H9 Cell Line	embryonic stem cell
14	chr5:177982000-177982800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr5:177982000-177983200	Enhancers	Left Ventricle	heart
16	chr5:177982000-177983400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:177982000-177983400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:177982000-177983600	Enhancers	Fetal Heart	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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