Variant report

Variant	rs7969844
Chromosome Location	chr12:58278271-58278272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58257740..58261779-chr12:58273700..58278459,4	MCF-7	breast:
2	chr12:58277381..58280585-chr12:58285894..58289659,5	MCF-7	breast:
3	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245651	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10444569	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747784	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10747786	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747787	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783854	0.80[ASN][1000 genomes]
rs10783855	0.81[ASN][1000 genomes]
rs10783856	0.81[ASN][1000 genomes]
rs10877029	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877030	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877031	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877032	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172367	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172368	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172369	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172371	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172378	0.81[ASN][1000 genomes]
rs12312955	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12319233	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12426201	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1599750	0.83[AMR][1000 genomes]
rs1599751	0.83[AMR][1000 genomes]
rs1599931	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1962047	0.81[ASN][1000 genomes]
rs2002275	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3751331	0.81[ASN][1000 genomes]
rs4237844	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760172	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760339	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760340	0.83[ASN][1000 genomes]
rs4760341	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs5017863	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59401446	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581157	0.82[ASN][1000 genomes]
rs7134797	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7312623	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9645819	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7969844	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs7969844	XRCC6BP1	cis	lung	GTEx
rs7969844	XRCC6BP1	cis	Whole Blood	GTEx
rs7969844	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs7969844	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs7969844	XRCC6BP1	cis	Artery Aorta	GTEx
rs7969844	XRCC6BP1	cis	Artery Tibial	GTEx
rs7969844	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs7969844	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7969844	TSFM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58270400-58280600	Weak transcription	Colonic Mucosa	Colon
2	chr12:58275400-58281600	Weak transcription	Esophagus	oesophagus
3	chr12:58275600-58280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:58275600-58280400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:58275600-58280400	Weak transcription	Fetal Heart	heart
6	chr12:58275600-58280400	Weak transcription	NHDF-Ad	bronchial
7	chr12:58275600-58280400	Weak transcription	NHLF	lung
8	chr12:58275800-58280400	Weak transcription	Right Atrium	heart
9	chr12:58275800-58280800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:58276000-58280400	Weak transcription	Left Ventricle	heart
11	chr12:58276000-58281600	Weak transcription	Hela-S3	cervix
12	chr12:58276000-58281800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:58276800-58280200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:58276800-58280400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:58277000-58280400	Weak transcription	Psoas Muscle	Psoas
16	chr12:58277600-58280400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:58277600-58280800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:58277800-58280400	Weak transcription	Rectal Mucosa Donor 29	rectum

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