Variant report

Variant	rs6710659
Chromosome Location	chr2:73607510-73607511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73605402..73609183-chr2:73611183..73613614,6	MCF-7	breast:
2	chr2:73605670..73609629-chr2:73611404..73613842,4	K562	blood:
3	chr2:73605602..73610192-chr2:73611523..73615241,7	K562	blood:
4	chr2:73606604..73608316-chr2:73620841..73623295,2	K562	blood:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10165862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10175529	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190002	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1083922	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs10865398	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11126395	0.83[ASN][1000 genomes]
rs11126396	0.83[ASN][1000 genomes]
rs11126399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693531	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11898362	0.83[ASN][1000 genomes]
rs11899902	0.82[AMR][1000 genomes]
rs12465867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13428235	0.82[AMR][1000 genomes]
rs1403412	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1406105	0.91[CHB][hapmap]
rs1522926	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1851546	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1852644	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs1881246	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1881247	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2017116	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2037814	1.00[CHB][hapmap]
rs2091022	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2421489	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2421545	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2421546	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2901437	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35885918	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820700	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs56672945	0.82[AMR][1000 genomes]
rs60844734	0.82[AMR][1000 genomes]
rs6546824	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546826	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546827	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6706235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6706409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716776	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6728128	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6747145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6748040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6749680	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs7560272	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7567017	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7567343	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7573275	0.84[ASN][1000 genomes]
rs7574291	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs7576824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7598901	0.92[CHB][hapmap]
rs7604588	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs780396	1.00[CHB][hapmap];0.81[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	nsv2778	chr2:73596272-73615138	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6710659	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs6710659	ALMS1P	cis	Whole Blood	GTEx
rs6710659	ALMS1	cis	Whole Blood	GTEx
rs6710659	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs6710659	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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