Variant report

Variant	rs1557857
Chromosome Location	chr7:120573642-120573643
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120572871..120575820-chr7:120582834..120585642,2	K562	blood:
2	chr7:120567399..120568924-chr7:120573182..120576035,2	K562	blood:
3	chr7:120570512..120572565-chr7:120572771..120574747,2	MCF-7	breast:
4	chr7:120558221..120561390-chr7:120571663..120574345,3	MCF-7	breast:
5	chr7:120569011..120571140-chr7:120572533..120574457,3	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10225453	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10238554	0.89[ASN][1000 genomes]
rs10252911	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10257297	0.83[ASN][1000 genomes]
rs10257475	0.82[ASN][1000 genomes]
rs10261886	0.80[ASN][1000 genomes]
rs10266755	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10272601	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10274689	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10279837	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10282072	0.89[ASN][1000 genomes]
rs10953922	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11982493	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13438082	0.80[ASN][1000 genomes]
rs17142995	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs17143001	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs17143009	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs17143055	0.80[ASN][1000 genomes]
rs1859316	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1859318	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040762	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2074577	0.80[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2097806	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2107276	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2244863	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2244865	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2248890	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2524949	0.86[EUR][1000 genomes]
rs2524951	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525705	0.90[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525708	0.87[ASN][1000 genomes]
rs2525709	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525710	0.85[CEU][hapmap]
rs2525712	0.81[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2525713	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2525719	0.82[ASN][1000 genomes]
rs2525730	0.82[ASN][1000 genomes]
rs2525737	0.82[ASN][1000 genomes]
rs2525743	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2721330	0.86[CEU][hapmap]
rs2721332	0.81[CEU][hapmap]
rs2721339	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2721341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2721343	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2721346	0.80[CEU][hapmap]
rs2721347	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2721354	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721363	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2721364	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721365	0.82[ASN][1000 genomes]
rs2721367	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2721372	0.82[ASN][1000 genomes]
rs3757556	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3779386	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3823859	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3823861	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs41624	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs41629	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs41632	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs41690	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4461820	0.80[ASN][1000 genomes]
rs61452531	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466759	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6466760	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6466761	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6466762	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6953454	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6958947	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6959328	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6964344	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6971854	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6975372	0.80[ASN][1000 genomes]
rs6979247	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs714259	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs732568	0.87[ASN][1000 genomes]
rs73427866	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73429803	0.82[ASN][1000 genomes]
rs745167	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7776721	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7781985	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9649429	0.82[ASN][1000 genomes]
rs996903	0.95[CHB][hapmap];0.95[JPT][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1557857	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120571600-120574000	Enhancers	HUVEC	blood vessel
2	chr7:120573600-120573800	Flanking Bivalent TSS/Enh	Sigmoid Colon	Sigmoid Colon
3	chr7:120573600-120574000	Enhancers	Colon Smooth Muscle	Colon
4	chr7:120573600-120574200	Enhancers	Fetal Intestine Large	intestine
5	chr7:120573600-120574400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:120573600-120574400	Enhancers	Rectal Smooth Muscle	rectum

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