Variant report

Variant	rs13212562
Chromosome Location	chr6:27300310-27300311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27298779..27303006-chr6:27440534..27442735,4	K562	blood:
2	chr6:27273015..27275740-chr6:27298464..27301159,2	K562	blood:
3	chr6:27299766..27302375-chr6:27444830..27446395,2	K562	blood:
4	chr6:27298898..27303175-chr6:27340830..27343404,5	K562	blood:
5	chr6:27287824..27293332-chr6:27295713..27302247,8	K562	blood:
6	chr6:27291413..27293040-chr6:27299829..27302713,2	MCF-7	breast:
7	chr6:27277495..27280431-chr6:27299498..27302391,2	K562	blood:
8	chr6:27263999..27267440-chr6:27299677..27302604,5	K562	blood:
9	chr6:27276791..27280576-chr6:27298923..27302888,5	K562	blood:
10	chr6:27299407..27301409-chr6:27341654..27343404,2	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000158553	Chromatin interaction
ENSG00000220758	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs13191227	0.80[EUR][1000 genomes]
rs13196692	0.80[EUR][1000 genomes]
rs13207082	0.80[EUR][1000 genomes]
rs13207689	0.82[EUR][1000 genomes]
rs13218537	0.80[EUR][1000 genomes]
rs28360634	0.86[EUR][1000 genomes]
rs34071253	0.82[EUR][1000 genomes]
rs34332556	0.80[EUR][1000 genomes]
rs34953377	0.80[EUR][1000 genomes]
rs35120058	0.80[EUR][1000 genomes]
rs35716472	0.82[EUR][1000 genomes]
rs41473150	0.90[CHB][hapmap];0.96[ASN][1000 genomes]
rs56114371	0.80[EUR][1000 genomes]
rs56401801	0.91[EUR][1000 genomes]
rs66841633	0.80[EUR][1000 genomes]
rs67859638	0.82[EUR][1000 genomes]
rs71537559	0.89[EUR][1000 genomes]
rs72839445	0.80[EUR][1000 genomes]
rs72839477	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv883507	chr6:27279982-27318836	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2761047	chr6:27296775-27303927	Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13212562	BTN3A2	cis	Thyroid	GTEx
rs13212562	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs13212562	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13212562	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs13212562	BTN3A2	cis	Nerve Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27299000-27300600	Enhancers	HepG2	liver
2	chr6:27299200-27300400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:27299400-27300400	Weak transcription	K562	blood
4	chr6:27300200-27300400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr6:27300200-27303200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:27300200-27303400	Active TSS	HUES48 Cell Line	embryonic stem cell

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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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