Variant report

Variant	rs1540053
Chromosome Location	chr4:100082154-100082155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADH4-1	chr4:100081671-100082422	NONHSAT097522
2	lnc-ADH4-1	chr4:100081751-100082804	NONHSAT097523
3	lnc-ADH4-1	chr4:100082094-100082802	NONHSAT097524

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10017466	1.00[CHD][hapmap]
rs10024157	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10470964	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1126670	1.00[CHD][hapmap]
rs1126671	1.00[CHD][hapmap]
rs1126673	1.00[CHD][hapmap]
rs1230155	0.81[GIH][hapmap]
rs1573495	1.00[CHD][hapmap]
rs1893881	1.00[CHD][hapmap]
rs2032345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2032349	1.00[CHD][hapmap]
rs2097122	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4141887	1.00[CHD][hapmap];0.81[YRI][hapmap]
rs4148883	0.88[ASW][hapmap];0.88[YRI][hapmap]
rs4699720	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6532798	1.00[CHD][hapmap]
rs6532800	1.00[CHD][hapmap]
rs6837685	1.00[CHD][hapmap]
rs6845578	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6855482	1.00[CHD][hapmap]
rs7678890	0.89[YRI][hapmap]
rs7678936	0.82[ASW][hapmap];1.00[CHD][hapmap];0.89[YRI][hapmap]
rs9307234	1.00[CHD][hapmap]

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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv879657	chr4:100082154-100139366	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1540053	C4orf37	cis	parietal	SCAN
rs1540053	ADH1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100035000-100098200	Weak transcription	Ovary	ovary
2	chr4:100056800-100082600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:100064000-100082600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:100065600-100096600	Weak transcription	Fetal Lung	lung
5	chr4:100066200-100083200	Enhancers	Liver	Liver
6	chr4:100066600-100082600	Weak transcription	Pancreas	Pancrea
7	chr4:100072200-100101400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:100074600-100085400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:100075600-100083200	Enhancers	HepG2	liver
10	chr4:100078800-100088400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:100079800-100082600	Weak transcription	Aorta	Aorta
12	chr4:100082000-100082800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:100082000-100083200	Enhancers	Fetal Intestine Large	intestine

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