Variant report

Variant	rs2300049
Chromosome Location	chr7:108068729-108068730
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10230518	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1034825	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1034829	0.86[JPT][hapmap]
rs11983030	0.81[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13221639	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1990162	0.87[CEU][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2284290	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]
rs2284291	0.85[JPT][hapmap]
rs2300037	0.81[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2300043	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	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300053	0.86[JPT][hapmap]
rs4141076	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4730320	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61550883	0.82[AFR][1000 genomes];0.82[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2300049	NRCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 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	chr7:108057600-108069000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:108058800-108071200	Weak transcription	Pancreas	Pancrea
4	chr7:108059800-108073400	Weak transcription	Fetal Brain Female	brain
5	chr7:108063200-108070400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:108065000-108070000	Enhancers	A549	lung
7	chr7:108065000-108071000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:108067000-108069600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:108067000-108071000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:108067200-108070800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:108067400-108069400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:108067400-108071200	Weak transcription	HMEC	breast
13	chr7:108067600-108081000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:108067800-108068800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:108067800-108089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:108068000-108069200	Enhancers	HUVEC	blood vessel
17	chr7:108068000-108089400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:108068400-108068800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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