Variant report

Variant	rs2530123
Chromosome Location	chr7:97474341-97474342
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1229564	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1234947	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1237625	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2457585	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2457586	0.82[ASN][1000 genomes]
rs2530121	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530122	0.83[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2665438	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6959868	0.82[ASN][1000 genomes]
rs6971012	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs71563539	0.88[AFR][1000 genomes]
rs71563540	0.88[AFR][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	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv428178	chr7:97402756-97648029	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2530123	GAL3ST4	cis	cerebellum	SCAN
rs2530123	PILRB	cis	parietal	SCAN
rs2530123	GJC3	cis	parietal	SCAN
rs2530123	SPDYE3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97472800-97483000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:97473000-97480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:97473400-97480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr7:97474200-97474400	Enhancers	Brain Germinal Matrix	brain

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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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