Variant report

Variant	rs17143009
Chromosome Location	chr7:120504978-120504979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120500977..120503177-chr7:120504931..120507716,4	K562	blood:
2	chr7:120504054..120506275-chr7:120506621..120509574,2	K562	blood:
3	chr7:120504448..120506162-chr7:120510454..120511972,2	K562	blood:
4	chr7:120493325..120495298-chr7:120504953..120507173,2	K562	blood:
5	chr7:120495753..120498197-chr7:120502989..120505087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106025	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10225453	0.85[CEU][hapmap]
rs10261886	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs10274689	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10279837	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11976580	0.85[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs11982493	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17132716	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs17132731	0.85[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs17142976	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs17142995	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs17143001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17143013	0.85[EUR][1000 genomes]
rs17143055	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1859319	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2040762	0.81[EUR][1000 genomes]
rs2097806	0.86[CEU][hapmap]
rs2158323	0.87[ASN][1000 genomes]
rs2158324	0.87[ASN][1000 genomes]
rs2189452	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2248890	0.85[CEU][hapmap]
rs2402551	0.87[ASN][1000 genomes]
rs2524949	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2721341	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs2721343	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2721344	0.84[EUR][1000 genomes]
rs2721346	0.80[CEU][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs2721347	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2721354	0.85[CEU][hapmap]
rs3757557	0.90[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3779387	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs3779388	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3779389	0.85[CHB][hapmap]
rs3823859	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4141309	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4461820	0.85[CHB][hapmap]
rs56023697	0.86[EUR][1000 genomes]
rs56755229	0.82[ASN][1000 genomes]
rs56922360	0.83[ASN][1000 genomes]
rs57457261	0.83[ASN][1000 genomes]
rs57818444	0.82[ASN][1000 genomes]
rs59169713	0.83[ASN][1000 genomes]
rs59567952	0.81[ASN][1000 genomes]
rs61043018	0.82[ASN][1000 genomes]
rs6466759	0.85[CEU][hapmap]
rs6466760	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs6466761	0.85[CEU][hapmap]
rs6466762	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs67679138	0.81[EUR][1000 genomes]
rs6958947	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6959328	0.85[CEU][hapmap]
rs6975372	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs714259	0.90[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73427831	0.81[ASN][1000 genomes]
rs73427834	0.82[ASN][1000 genomes]
rs73427862	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73427866	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73427871	0.86[EUR][1000 genomes]
rs73427873	0.86[EUR][1000 genomes]
rs73427878	0.85[EUR][1000 genomes]
rs73721472	0.87[EUR][1000 genomes]
rs7779136	0.83[ASN][1000 genomes]
rs7779149	0.83[ASN][1000 genomes]
rs7779941	0.83[ASN][1000 genomes]
rs7780247	0.83[ASN][1000 genomes]
rs7781985	0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs7806629	0.83[ASN][1000 genomes]
rs7810542	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs886440	0.85[CEU][hapmap]
rs9648991	0.82[ASN][1000 genomes]
rs9648992	0.83[ASN][1000 genomes]
rs9648993	0.83[ASN][1000 genomes]
rs9649427	0.83[ASN][1000 genomes]
rs9649428	0.82[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
rs17143009	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120498400-120506800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:120504200-120505200	Enhancers	Fetal Muscle Leg	muscle
3	chr7:120504200-120505800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:120504400-120505800	Enhancers	HSMMtube	muscle
5	chr7:120504400-120506000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:120504400-120506800	Enhancers	Fetal Heart	heart
7	chr7:120504600-120505000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:120504600-120505000	Enhancers	Right Atrium	heart
9	chr7:120504600-120505000	Enhancers	Right Ventricle	heart
10	chr7:120504600-120505600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:120504600-120505600	Enhancers	Fetal Kidney	kidney
12	chr7:120504600-120506000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:120504800-120506000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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