Variant report

Variant	rs404240
Chromosome Location	chr6:29523957-29523958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1233385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1233393	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1233493	0.89[EUR][1000 genomes]
rs1233494	0.89[EUR][1000 genomes]
rs1234844	0.89[EUR][1000 genomes]
rs2023463	0.89[EUR][1000 genomes]
rs2143668	0.91[EUR][1000 genomes]
rs2523431	0.91[EUR][1000 genomes]
rs2523432	0.83[EUR][1000 genomes]
rs2523443	0.91[EUR][1000 genomes]
rs2746149	0.89[EUR][1000 genomes]
rs2746150	0.91[EUR][1000 genomes]
rs3094569	0.81[EUR][1000 genomes]
rs3131856	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3131894	1.00[AFR][1000 genomes]
rs408623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs404240	ZNF323	cis	parietal	SCAN
rs404240	HIST1H2BC	cis	parietal	SCAN
rs404240	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs404240	BTN2A1	cis	parietal	SCAN
rs404240	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs404240	BTN3A2	trans	lymphoblastoid	seeQTL
rs404240	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs404240	HIST1H2BM	cis	cerebellum	SCAN
rs404240	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29523800-29524000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29523800-29524000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
3	chr6:29523800-29524000	Enhancers	Spleen	Spleen

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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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