Variant report

Variant	rs12312955
Chromosome Location	chr12:58265223-58265224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58236905..58239639-chr12:58262995..58265334,2	MCF-7	breast:
2	chr12:58263220..58265697-chr12:58267333..58269634,2	MCF-7	breast:
3	chr12:58237087..58244044-chr12:58260690..58267738,8	K562	blood:
4	chr12:58240989..58243602-chr12:58264748..58266255,2	MCF-7	breast:
5	chr12:58259629..58265686-chr12:58266089..58272179,8	K562	blood:
6	chr12:58240495..58242437-chr12:58263947..58265821,2	MCF-7	breast:
7	chr12:58255940..58258991-chr12:58263646..58265441,3	K562	blood:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10444569	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10747784	0.82[EUR][1000 genomes]
rs10747786	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747787	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783850	0.84[AMR][1000 genomes]
rs10783851	0.84[AMR][1000 genomes]
rs10783854	0.87[AMR][1000 genomes]
rs10783855	0.88[AMR][1000 genomes]
rs10783856	0.85[AMR][1000 genomes]
rs10877024	0.84[AMR][1000 genomes]
rs10877025	0.84[AMR][1000 genomes]
rs10877026	0.83[AMR][1000 genomes]
rs10877029	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877030	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877031	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877032	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172367	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172368	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172369	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172371	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12319233	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12426201	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1599750	0.85[AMR][1000 genomes]
rs1599751	0.85[AMR][1000 genomes]
rs1599931	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1875125	0.83[AMR][1000 genomes]
rs2002275	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4237844	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760172	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760339	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760341	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5017863	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59401446	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7134797	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7312623	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969844	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9645819	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[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
rs12312955	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs12312955	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs12312955	XRCC6BP1	cis	Artery Tibial	GTEx
rs12312955	METTL21B	cis	lung	GTEx
rs12312955	XRCC6BP1	cis	Whole Blood	GTEx
rs12312955	XRCC6BP1	cis	lung	GTEx
rs12312955	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12312955	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs12312955	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs12312955	XRCC6BP1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58259400-58269600	Weak transcription	Aorta	Aorta
2	chr12:58259600-58267800	Weak transcription	Colonic Mucosa	Colon
3	chr12:58259600-58268000	Weak transcription	Left Ventricle	heart
4	chr12:58259800-58267600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:58262400-58269600	Weak transcription	Fetal Heart	heart
6	chr12:58262800-58267000	Weak transcription	Right Atrium	heart
7	chr12:58262800-58267800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:58263000-58269800	Weak transcription	Lung	lung
9	chr12:58263200-58271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:58263400-58267600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:58263600-58267600	Weak transcription	Adipose Nuclei	Adipose
12	chr12:58263600-58269600	Weak transcription	NHLF	lung
13	chr12:58263600-58275000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:58263800-58269600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:58264000-58267600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:58264000-58268600	Weak transcription	Placenta	Placenta
17	chr12:58264000-58269600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:58264200-58266000	Weak transcription	Psoas Muscle	Psoas
19	chr12:58264200-58268000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:58264400-58267000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:58264400-58267600	Weak transcription	Brain Angular Gyrus	brain
22	chr12:58264400-58267600	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:58264400-58267800	Weak transcription	Fetal Stomach	stomach
24	chr12:58264400-58268600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:58264400-58269600	Weak transcription	Brain Substantia Nigra	brain
26	chr12:58264400-58269600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:58264400-58269800	Weak transcription	Brain Anterior Caudate	brain
28	chr12:58264600-58265800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:58264600-58265800	Weak transcription	Fetal Brain Female	brain
30	chr12:58264600-58267000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:58264600-58267800	Weak transcription	Fetal Lung	lung
32	chr12:58264600-58267800	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:58264600-58268400	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:58265200-58265600	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links