Variant report

Variant	rs7747216
Chromosome Location	chr6:33476718-33476719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11752501	0.85[ASN][1000 genomes]
rs11752508	0.85[ASN][1000 genomes]
rs11757081	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs11759461	0.85[ASN][1000 genomes]
rs35131737	0.85[ASN][1000 genomes]
rs3857557	0.88[ASN][1000 genomes]
rs4428487	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713632	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55659258	0.85[ASN][1000 genomes]
rs55683509	0.85[ASN][1000 genomes]
rs62405865	0.85[ASN][1000 genomes]
rs62405866	0.85[ASN][1000 genomes]
rs62405867	0.85[ASN][1000 genomes]
rs62405887	0.85[ASN][1000 genomes]
rs62405896	0.88[ASN][1000 genomes]
rs62405899	0.88[ASN][1000 genomes]
rs62405900	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6911036	0.88[ASN][1000 genomes]
rs6942274	0.85[ASN][1000 genomes]
rs769051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743060	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743064	0.85[ASN][1000 genomes]
rs7743178	0.85[ASN][1000 genomes]
rs7743445	0.85[ASN][1000 genomes]
rs7748370	0.85[ASN][1000 genomes]
rs9296092	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366823	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380362	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380364	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380366	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394153	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv521506	chr6:33468151-33480738	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv524010	chr6:33468151-33505981	Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Age at smoking initiation in chronic obstructive pulmonary disease	21685187	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7747216	LHFPL5	cis	parietal	SCAN
rs7747216	CDKN1A	cis	parietal	SCAN
rs7747216	C6orf129	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33473800-33476800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:33474200-33476800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:33474200-33476800	Weak transcription	Adipose Nuclei	Adipose
4	chr6:33474200-33477000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:33474400-33476800	Weak transcription	Right Atrium	heart
6	chr6:33474400-33476800	Weak transcription	K562	blood
7	chr6:33474400-33477000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:33474400-33481200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:33474600-33477000	Weak transcription	Fetal Heart	heart
10	chr6:33476000-33477200	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:33476200-33476800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr6:33476400-33476800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:33476400-33477000	Weak transcription	Spleen	Spleen
14	chr6:33476600-33476800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:33476600-33476800	Enhancers	Primary B cells from cord blood	blood
16	chr6:33476600-33476800	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:33476600-33476800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr6:33476600-33476800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:33476600-33476800	Active TSS	Fetal Kidney	kidney
20	chr6:33476600-33477200	Flanking Active TSS	GM12878-XiMat	blood
21	chr6:33476600-33477600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:33476600-33477600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr6:33476600-33479800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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