Variant report

Variant	rs2300043
Chromosome Location	chr7:108063095-108063096
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10230518	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1034825	0.86[JPT][hapmap]
rs1034829	0.86[JPT][hapmap]
rs11983030	0.89[ASW][hapmap];0.88[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12333431	0.84[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13221639	0.83[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs1990162	0.92[CEU][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108256	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2158846	0.81[MKK][hapmap]
rs2284290	0.89[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2284291	0.84[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2300037	0.87[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2300045	0.87[GIH][hapmap];0.84[MEX][hapmap]
rs2300049	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300050	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300053	0.86[JPT][hapmap]
rs4141076	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4730307	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4730309	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4730320	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs61550883	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs917251	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2300043	LHFPL3	cis	parietal	SCAN
rs2300043	NRCAM	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108056800-108071000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:108057200-108067200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:108057600-108065800	Weak transcription	NHEK	skin
4	chr7:108057600-108066000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:108057600-108067000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:108057600-108069000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:108057800-108064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:108058800-108067400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:108058800-108071200	Weak transcription	Pancreas	Pancrea
10	chr7:108059800-108073400	Weak transcription	Fetal Brain Female	brain
11	chr7:108061200-108067000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:108061600-108063200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:108061600-108064000	Enhancers	HUVEC	blood vessel
14	chr7:108062000-108063200	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr7:108062800-108066800	Weak transcription	Brain Angular Gyrus	brain
16	chr7:108063000-108064400	Enhancers	A549	lung

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