Variant report

Variant	rs1673409
Chromosome Location	chr8:110531770-110531771
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:110531701-110531783	Lung_OC	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:110531754..110534652-chr8:110551713..110553240,2	MCF-7	breast:
2	chr8:110531365..110533203-chr8:110533414..110535104,2	K562	blood:
3	chr8:110531770..110532745-chr8:110563872..110564774,2	MCF-7	breast:
4	chr8:110530935..110534382-chr8:110534655..110537155,3	MCF-7	breast:

Variant related genes	Relation type
PKHD1L1	TF binding region
ENSG00000205038	Chromatin interaction
ENSG00000147654	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10088258	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10088612	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10088684	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1009371	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10108943	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10111682	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1013482	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1026437	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1044230	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10505133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13249244	0.97[ASN][1000 genomes]
rs13439318	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13439864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1379361	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1379366	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1379367	0.90[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1457282	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[ASN][1000 genomes]
rs1457283	0.91[ASN][1000 genomes]
rs1457288	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1457294	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1457295	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563580	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1617259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1617350	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1626759	0.87[ASW][hapmap];0.86[YRI][hapmap]
rs1630134	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[ASN][1000 genomes]
rs1630942	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1673383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673386	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673411	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1673412	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1673413	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673415	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1673416	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs1673419	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1673420	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs1673421	0.90[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs1673422	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1673424	0.95[ASN][1000 genomes]
rs1673425	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1673426	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1673427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17377636	0.97[ASN][1000 genomes]
rs17449762	0.97[ASN][1000 genomes]
rs1783140	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1783141	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1783147	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1783148	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1783153	0.90[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs1783154	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1783155	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1783157	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1783158	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1783159	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs1783161	0.95[ASN][1000 genomes]
rs1783162	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1783166	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1783167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783168	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1783169	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1783170	0.91[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1783171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783172	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783173	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1783174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783175	0.97[ASN][1000 genomes]
rs1870389	0.84[MEX][hapmap]
rs1892759	0.94[JPT][hapmap]
rs1892760	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2022934	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2022935	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2154658	0.94[JPT][hapmap]
rs2154660	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236627	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2236628	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2607624	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607627	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2607628	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2607629	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2607630	0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.95[ASN][1000 genomes]
rs2607631	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2607632	0.92[ASN][1000 genomes]
rs2607633	0.93[ASW][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[ASN][1000 genomes]
rs2607635	0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2607636	0.92[ASN][1000 genomes]
rs2703377	0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs2703382	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2703384	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2703386	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2703387	0.86[ASN][1000 genomes]
rs2703388	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2703389	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2844231	0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2844234	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2844235	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2844236	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2844254	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs2844255	0.92[ASN][1000 genomes]
rs2844256	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2844257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844260	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926239	0.85[MEX][hapmap]
rs2980571	0.90[MEX][hapmap]
rs3808380	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4529437	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6995356	0.97[ASN][1000 genomes]
rs7006166	0.95[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs7011340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7011803	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs720139	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs720140	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs730885	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753995	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7818726	0.87[ASN][1000 genomes]
rs7821242	0.97[ASN][1000 genomes]
rs897840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930877	0.92[ASN][1000 genomes]

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	nsv891281	chr8:110450092-110558622	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1673409	PKHD1L1	cis	multi-tissue	Pritchard
rs1673409	PKHD1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110526600-110532400	Weak transcription	K562	blood
2	chr8:110531000-110535000	Enhancers	Primary B cells from peripheral blood	blood
3	chr8:110531600-110534200	Enhancers	GM12878-XiMat	blood

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