Variant report

Variant	rs2284290
Chromosome Location	chr7:108074766-108074767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10230518	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1034825	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1034829	0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11983030	0.91[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs12333431	0.91[MEX][hapmap]
rs13221639	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1990162	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2284291	0.91[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs2284292	0.81[ASN][1000 genomes]
rs2300037	0.81[JPT][hapmap];0.80[YRI][hapmap]
rs2300043	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]
rs2300049	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300050	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300053	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3763462	0.86[CHB][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs4730320	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6976478	0.81[ASN][1000 genomes]
rs726471	0.85[GIH][hapmap]
rs917251	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]

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
rs2284290	NRCAM	Cis_1M	lymphoblastoid	RTeQTL
rs2284290	LHFPL3	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108067600-108081000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:108067800-108089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:108068000-108089400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:108069000-108086000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:108071800-108074800	Weak transcription	Brain Anterior Caudate	brain
6	chr7:108071800-108075200	Weak transcription	HMEC	breast
7	chr7:108072000-108074800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:108072000-108075800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:108072600-108075200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:108073600-108075000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:108073600-108075200	Enhancers	Pancreas	Pancrea
12	chr7:108074000-108075400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:108074000-108075400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr7:108074200-108075200	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr7:108074400-108074800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:108074400-108075200	Enhancers	HUVEC	blood vessel
17	chr7:108074600-108076400	Enhancers	A549	lung

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

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