Variant report

Variant	rs56023697
Chromosome Location	chr7:120503085-120503086
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120496585..120499423-chr7:120501115..120503744,3	K562	blood:
2	chr7:120501243..120503958-chr7:120508680..120510304,2	K562	blood:
3	chr7:120500977..120503177-chr7:120504931..120507716,4	K562	blood:
4	chr7:120495753..120498197-chr7:120502989..120505087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106025	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs114420	0.86[ASN][1000 genomes]
rs11976580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673417	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17132731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17142976	0.93[ASN][1000 genomes]
rs17143001	0.86[EUR][1000 genomes]
rs17143009	0.86[EUR][1000 genomes]
rs17143013	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189974	0.86[ASN][1000 genomes]
rs2525706	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2525710	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2721329	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2721330	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2721332	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721344	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721346	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721348	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721360	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721371	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41613	0.93[ASN][1000 genomes]
rs41616	0.93[ASN][1000 genomes]
rs41617	0.93[ASN][1000 genomes]
rs41622	0.93[ASN][1000 genomes]
rs41623	0.93[ASN][1000 genomes]
rs41626	0.93[ASN][1000 genomes]
rs42333	0.93[ASN][1000 genomes]
rs4730982	0.93[ASN][1000 genomes]
rs55733320	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55749650	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56067931	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61481874	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67679138	0.93[ASN][1000 genomes]
rs73427862	0.86[EUR][1000 genomes]
rs73427871	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73427873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73427878	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73721472	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7805733	0.93[ASN][1000 genomes]
rs7810542	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs886440	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56023697	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120498400-120504600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:120498400-120506800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:120499000-120503200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:120499000-120504600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:120499000-120504800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:120499200-120504400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:120499400-120504600	Weak transcription	Fetal Kidney	kidney
8	chr7:120499800-120504400	Weak transcription	Fetal Heart	heart
9	chr7:120502000-120503400	Enhancers	Fetal Muscle Leg	muscle
10	chr7:120503000-120503200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:120503000-120503400	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links