Variant report

Variant	rs3763462
Chromosome Location	chr7:108098201-108098202
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr7:108098018-108098249	A549	lung:	n/a	chr7:108098183-108098194
2	CEBPB	chr7:108098114-108098233	K562	blood:	n/a	chr7:108098183-108098194

No.	Distal block	Cell Line	Cell type
1	chr7:107996666..108000210-chr7:108094187..108098858,6	MCF-7	breast:
2	chr7:107998008..108001072-chr7:108096682..108098603,3	MCF-7	breast:
3	chr7:107817682..107823715-chr7:108094168..108099407,9	MCF-7	breast:
4	chr7:107823921..107826218-chr7:108097722..108100120,2	MCF-7	breast:

Variant related genes	Relation type
NRCAM	TF binding region
ENSG00000091129	Chromatin interaction
ENSG00000266112	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10230518	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10273997	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10278246	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1034825	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1034829	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13221639	0.86[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13244602	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1473131	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17339110	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1859769	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1859771	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1859772	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1859774	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1859775	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs194585	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs194586	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2214916	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284290	0.86[CHB][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs2284291	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2284292	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2300053	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2396001	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815252	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs40846	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs40849	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs40856	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs40890	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs40903	0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[EUR][1000 genomes]
rs6466239	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6466240	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6966431	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6976478	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs726471	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73426110	0.94[EUR][1000 genomes]
rs7800334	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7806223	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs917251	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9640707	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9785006	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	esv3358442	chr7:108095941-108098489	Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3763462	LHFPL3	cis	parietal	SCAN
rs3763462	C7orf66	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108097200-108100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:108097200-108118000	Weak transcription	Aorta	Aorta
3	chr7:108097400-108100000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:108097800-108098400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:108097800-108098400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr7:108097800-108100000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:108097800-108100400	Weak transcription	HUVEC	blood vessel
8	chr7:108097800-108101400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:108097800-108101600	Weak transcription	Pancreas	Pancrea
10	chr7:108097800-108103200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr7:108098000-108101200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:108098200-108098400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
13	chr7:108098200-108098400	Weak transcription	Spleen	Spleen
14	chr7:108098200-108098600	Weak transcription	A549	lung
15	chr7:108098200-108100400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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