Variant report

Variant	rs4553410
Chromosome Location	chr12:58301211-58301212
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58257274..58258886-chr12:58300029..58301965,2	MCF-7	breast:
2	chr12:58174946..58176646-chr12:58299150..58302148,2	K562	blood:
3	chr12:58299276..58301907-chr12:58305414..58307354,2	MCF-7	breast:
4	chr12:58299223..58301569-chr12:58315233..58317786,2	K562	blood:
5	chr12:58162344..58164434-chr12:58300601..58302220,2	MCF-7	breast:
6	chr12:58238650..58240724-chr12:58299517..58301616,2	K562	blood:
7	chr12:58238316..58242683-chr12:58295473..58302602,14	MCF-7	breast:
8	chr12:58176194..58177965-chr12:58301186..58302855,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000111012	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000123297	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10877033	0.91[ASN][1000 genomes]
rs10877034	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172372	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3751330	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4128707	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4237845	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4417327	0.93[ASN][1000 genomes]
rs6650217	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6650218	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6650219	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7306124	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7954591	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7954957	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7963992	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971877	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4553410	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4553410	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs4553410	XRCC6BP1	cis	Thyroid	GTEx
rs4553410	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs4553410	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4553410	XRCC6BP1	cis	Whole Blood	GTEx
rs4553410	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4553410	XRCC6BP1	cis	Artery Tibial	GTEx
rs4553410	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs4553410	XRCC6BP1	cis	Nerve Tibial	GTEx
rs4553410	XRCC6BP1	cis	lung	GTEx
rs4553410	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58300200-58303000	Weak transcription	Fetal Thymus	thymus
2	chr12:58300600-58301600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:58300800-58301400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:58301200-58301400	Enhancers	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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