Variant report

Variant	rs12162546
Chromosome Location	chr21:15976639-15976640
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1037807	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1292587	0.91[ASN][1000 genomes]
rs1380450	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2125755	0.82[JPT][hapmap]
rs2822809	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822828	0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs401697	0.90[ASN][1000 genomes]
rs439328	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs457188	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs458143	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs458711	0.85[ASN][1000 genomes]
rs459879	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs461178	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs461853	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs465122	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs466783	0.80[ASN][1000 genomes]
rs7277303	0.81[CHB][hapmap];0.91[JPT][hapmap]

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	nsv834045	chr21:15900678-16112850	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv834046	chr21:15903792-16077369	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15975200-15979600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr21:15975600-15984400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr21:15975800-15976800	Enhancers	Stomach Smooth Muscle	stomach
4	chr21:15975800-15979200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr21:15975800-15979400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr21:15975800-15979400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr21:15975800-15979400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr21:15975800-15979400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr21:15976000-15979400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr21:15976000-15979400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr21:15976000-15979800	Weak transcription	K562	blood
12	chr21:15976000-15980800	Weak transcription	Dnd41	blood
13	chr21:15976000-15981000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr21:15976200-15979400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr21:15976400-15979600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:15976600-15976800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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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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