Variant report

Variant	rs11574647
Chromosome Location	chr16:31394722-31394723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11150620	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11150621	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1140195	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2070896	0.84[EUR][1000 genomes]
rs28677987	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3892327	0.85[AMR][1000 genomes]
rs56191046	0.80[AMR][1000 genomes]
rs58724472	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59381569	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7188682	0.84[AMR][1000 genomes]
rs7199585	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8050328	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8052139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8055861	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9930811	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9936992	0.83[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
8	nsv1059610	chr16:31368699-31421660	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	esv3438651	chr16:31373520-31422007	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11574647	ITGAD	cis	multi-tissue	Pritchard
rs11574647	FBXL19	cis	cerebellum	SCAN
rs11574647	INO80E	cis	parietal	SCAN
rs11574647	AC026471.6	cis	lung	GTEx
rs11574647	AHSP	cis	parietal	SCAN
rs11574647	PRR14	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31343000-31400800	Weak transcription	Right Atrium	heart
2	chr16:31381000-31395000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr16:31387200-31395800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr16:31389400-31397400	Weak transcription	Pancreas	Pancrea
5	chr16:31391800-31396800	Weak transcription	Liver	Liver
6	chr16:31392200-31397000	Weak transcription	Esophagus	oesophagus
7	chr16:31392600-31398000	Weak transcription	Spleen	Spleen
8	chr16:31394000-31395800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:31394000-31397600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr16:31394200-31394800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr16:31394400-31397000	Weak transcription	A549	lung
12	chr16:31394600-31397000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr16:31394600-31397000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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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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