Variant report

Variant	rs29240
Chromosome Location	chr6:29607476-29607477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17178518	1.00[ASN][1000 genomes]
rs17178525	0.86[ASN][1000 genomes]
rs17178532	1.00[ASN][1000 genomes]
rs17184883	0.86[ASN][1000 genomes]
rs2747420	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs29234	0.86[ASN][1000 genomes]
rs29235	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs29238	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29272	0.86[ASN][1000 genomes]
rs3025623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909134	1.00[ASN][1000 genomes]
rs73747624	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461541	0.86[ASN][1000 genomes]
rs9468571	0.86[ASN][1000 genomes]
rs9468572	0.86[ASN][1000 genomes]
rs9500947	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv969292	chr6:29604881-29612154	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs29240	HLA-A	cis	lymphoblastoid	seeQTL
rs29240	LOC347981	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29601800-29608600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr6:29602600-29609200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:29602600-29609200	Weak transcription	HMEC	breast
4	chr6:29602800-29609200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:29603000-29608400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:29604200-29609200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:29606800-29607800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:29607000-29607600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr6:29607000-29607600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr6:29607000-29608400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:29607200-29607600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:29607200-29607600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:29607200-29608000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:29607400-29609200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:29607400-29609400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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