Variant report

Variant	rs2390479
Chromosome Location	chr7:21235197-21235198
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17143942	0.90[ASN][1000 genomes]
rs17143993	0.90[EUR][1000 genomes]
rs17143998	0.90[ASN][1000 genomes]
rs17144012	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17686402	0.83[EUR][1000 genomes]
rs1881960	0.90[ASN][1000 genomes]
rs2893031	0.90[ASN][1000 genomes]
rs3934483	0.90[ASN][1000 genomes]
rs4072217	0.90[ASN][1000 genomes]
rs4316063	0.81[ASN][1000 genomes]
rs4490733	0.90[ASN][1000 genomes]
rs55732235	0.89[EUR][1000 genomes]
rs55885414	0.90[ASN][1000 genomes]
rs56383835	0.90[ASN][1000 genomes]
rs58258104	0.90[ASN][1000 genomes]
rs58641677	0.90[ASN][1000 genomes]
rs59562853	0.81[ASN][1000 genomes]
rs59592870	0.90[ASN][1000 genomes]
rs60656967	0.81[ASN][1000 genomes]
rs61249337	0.90[ASN][1000 genomes]
rs61520146	0.90[ASN][1000 genomes]
rs61552779	0.90[ASN][1000 genomes]
rs73279571	0.90[ASN][1000 genomes]
rs73279573	0.90[ASN][1000 genomes]
rs73279575	0.90[ASN][1000 genomes]
rs73685044	0.81[ASN][1000 genomes]
rs7789062	0.90[ASN][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	esv3478244	chr7:21044211-21417347	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv3478245	chr7:21044211-21417347	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1020852	chr7:21060791-21375050	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538799	chr7:21060791-21375050	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2390479	IL6	cis	parietal	SCAN
rs2390479	CDCA7L	cis	cerebellum	SCAN
rs2390479	PRKCH	trans	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21233600-21235400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:21233600-21244400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:21234200-21235400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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