Variant report

Variant	rs11171632
Chromosome Location	chr12:56035456-56035457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10876836	1.00[CEU][hapmap]
rs10876837	1.00[CEU][hapmap];0.88[CHD][hapmap]
rs10876841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171623	0.87[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs11171625	1.00[CEU][hapmap]
rs11171626	1.00[CEU][hapmap]
rs11171629	0.81[EUR][1000 genomes]
rs11171631	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11171636	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11171638	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11171640	0.91[ASN][1000 genomes]
rs3858536	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4759184	0.84[ASN][1000 genomes]
rs58126534	0.95[ASN][1000 genomes]
rs7952953	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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	nsv559001	chr12:55507465-56057708	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3490751	chr12:56030785-56035633	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3490754	chr12:56031235-56035533	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3490750	chr12:56031555-56035542	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11171632	NFE2	cis	parietal	SCAN
rs11171632	OS9	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56023200-56036800	Weak transcription	Spleen	Spleen
2	chr12:56030800-56035800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:56032200-56036200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:56032600-56036000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:56032800-56040000	Weak transcription	Right Atrium	heart
6	chr12:56033800-56041400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:56034800-56035600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:56034800-56035800	Enhancers	Primary B cells from cord blood	blood
9	chr12:56034800-56037400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:56035000-56037400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr12:56035000-56037600	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:56035200-56038600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr12:56035400-56035600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:56035400-56035800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:56035400-56036200	Enhancers	GM12878-XiMat	blood
16	chr12:56035400-56036800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:56035400-56036800	Enhancers	Fetal Muscle Leg	muscle
18	chr12:56035400-56037400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:56035400-56040200	Weak transcription	Gastric	stomach

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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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