Variant report

Variant	rs10135054
Chromosome Location	chr14:71076460-71076461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71076190..71078982-chr14:71275139..71277878,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MED6-1	chr14:71075515-71078067	ENSG00000245466

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction
ENSG00000259153	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10142880	0.90[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10144849	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10145399	1.00[YRI][hapmap]
rs2233136	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs55638679	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55788982	0.80[ASN][1000 genomes]
rs55830682	0.80[ASN][1000 genomes]
rs55831916	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55844620	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55861611	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55988558	0.80[ASN][1000 genomes]
rs56118324	0.80[ASN][1000 genomes]
rs56284928	0.80[ASN][1000 genomes]
rs56322329	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56389452	0.80[ASN][1000 genomes]
rs56405439	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59480415	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66883325	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66915556	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67358716	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67988556	1.00[ASN][1000 genomes]
rs7150080	1.00[YRI][hapmap]
rs7153652	0.86[YRI][hapmap]
rs7154970	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7160103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72719730	0.80[ASN][1000 genomes]
rs72719731	0.80[ASN][1000 genomes]
rs72719734	0.80[ASN][1000 genomes]
rs72719735	0.80[ASN][1000 genomes]
rs72719738	0.80[ASN][1000 genomes]
rs72719739	0.80[ASN][1000 genomes]
rs72719741	0.80[ASN][1000 genomes]
rs72719743	0.80[ASN][1000 genomes]
rs72719744	0.80[ASN][1000 genomes]
rs72719746	0.80[ASN][1000 genomes]
rs72719747	0.80[ASN][1000 genomes]
rs72719748	0.80[ASN][1000 genomes]
rs72719750	0.80[ASN][1000 genomes]
rs72719751	0.80[ASN][1000 genomes]
rs72719754	0.90[ASN][1000 genomes]
rs72719757	0.90[ASN][1000 genomes]
rs72719758	0.90[ASN][1000 genomes]
rs72719764	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72719773	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72719777	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72719785	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719791	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73286047	0.83[AFR][1000 genomes]
rs73286048	0.83[AFR][1000 genomes]
rs8009390	1.00[YRI][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10135054	SIPA1L1	cis	lymphoblastoid	seeQTL
rs10135054	FRMD3	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71068400-71078600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:71069800-71076800	Weak transcription	GM12878-XiMat	blood

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