Variant report

Variant	rs12333431
Chromosome Location	chr7:108026243-108026244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11983030	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13221639	0.87[MEX][hapmap]
rs16872525	0.82[ASW][hapmap]
rs1990162	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2108256	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284290	0.91[MEX][hapmap]
rs2284291	0.83[MEX][hapmap]
rs2300037	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2300043	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]
rs2300045	0.81[GIH][hapmap]
rs4141076	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4730307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61550883	0.87[AMR][1000 genomes];0.93[EUR][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	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	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12333431	LHFPL3	cis	parietal	SCAN
rs12333431	NRCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108014800-108043200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:108020000-108034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:108021400-108040800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:108021400-108043000	Weak transcription	HMEC	breast
5	chr7:108021800-108026600	Weak transcription	HUVEC	blood vessel
6	chr7:108022400-108034200	Weak transcription	Pancreas	Pancrea
7	chr7:108024000-108033000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:108024000-108045600	Weak transcription	Brain Anterior Caudate	brain
9	chr7:108024200-108036000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:108024400-108034000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr7:108024400-108036000	Weak transcription	Brain Angular Gyrus	brain
12	chr7:108025400-108027600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr7:108025600-108034200	Weak transcription	A549	lung
14	chr7:108026000-108026800	Enhancers	GM12878-XiMat	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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