Variant report

Variant	rs10088684
Chromosome Location	chr8:110547656-110547657
allele	C/T
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	GATA1	chr8:110546842-110547694	PBDE	blood:	n/a	n/a
2	TEAD4	chr8:110547234-110547902	ECC-1	luminal epithelium:	n/a	n/a
3	MYC	chr8:110547190-110547756	MCF10A-Er-Src	breast:	n/a	chr8:110547400-110547409
4	NFIC	chr8:110547150-110547759	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:110546124..110548249-chr8:110656124..110658861,2	MCF-7	breast:
2	chr8:110346524..110348211-chr8:110547153..110549713,2	K562	blood:
3	chr8:110544819..110549449-chr8:110549976..110554355,13	K562	blood:

Variant related genes	Relation type
EBAG9	TF binding region
ENSG00000147654	Chromatin interaction
ENSG00000120526	Chromatin interaction
ENSG00000120533	Chromatin interaction
ENSG00000147642	Chromatin interaction
ENSG00000248050	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10088258	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10088612	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009371	0.91[ASN][1000 genomes]
rs10108943	0.98[ASN][1000 genomes]
rs10111682	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1013482	0.94[ASN][1000 genomes]
rs1026437	0.91[ASN][1000 genomes]
rs1044230	0.88[ASN][1000 genomes]
rs10505133	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13249244	0.98[ASN][1000 genomes]
rs13439318	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13439864	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379361	0.91[ASN][1000 genomes]
rs1379366	0.97[ASN][1000 genomes]
rs1379367	0.94[ASN][1000 genomes]
rs1457282	0.89[ASN][1000 genomes]
rs1457283	0.89[ASN][1000 genomes]
rs1457288	0.97[ASN][1000 genomes]
rs1457294	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1457295	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563578	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563580	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1617259	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617350	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630134	0.89[ASN][1000 genomes]
rs1630942	0.91[ASN][1000 genomes]
rs1673383	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673384	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673386	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1673389	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673395	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673399	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673409	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673410	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673411	0.97[ASN][1000 genomes]
rs1673413	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673415	0.97[ASN][1000 genomes]
rs1673416	0.96[ASN][1000 genomes]
rs1673419	0.97[ASN][1000 genomes]
rs1673420	0.97[ASN][1000 genomes]
rs1673421	0.95[ASN][1000 genomes]
rs1673424	0.94[ASN][1000 genomes]
rs1673425	0.94[ASN][1000 genomes]
rs1673426	0.94[ASN][1000 genomes]
rs1673427	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673428	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17377636	0.98[ASN][1000 genomes]
rs17449762	0.98[ASN][1000 genomes]
rs1783140	0.91[ASN][1000 genomes]
rs1783147	0.91[ASN][1000 genomes]
rs1783148	0.90[ASN][1000 genomes]
rs1783153	0.97[ASN][1000 genomes]
rs1783154	0.97[ASN][1000 genomes]
rs1783155	0.95[ASN][1000 genomes]
rs1783157	0.96[ASN][1000 genomes]
rs1783158	0.95[ASN][1000 genomes]
rs1783159	0.95[ASN][1000 genomes]
rs1783161	0.94[ASN][1000 genomes]
rs1783162	0.94[ASN][1000 genomes]
rs1783166	0.97[ASN][1000 genomes]
rs1783167	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783168	0.97[ASN][1000 genomes]
rs1783169	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783170	0.97[ASN][1000 genomes]
rs1783171	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783172	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783173	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783174	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783175	0.98[ASN][1000 genomes]
rs1892760	0.83[ASN][1000 genomes]
rs2022934	0.89[ASN][1000 genomes]
rs2022935	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2154660	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236627	0.84[ASN][1000 genomes]
rs2236628	0.83[ASN][1000 genomes]
rs2607624	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2607625	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2607627	0.94[ASN][1000 genomes]
rs2607628	0.94[ASN][1000 genomes]
rs2607629	0.94[ASN][1000 genomes]
rs2607630	0.94[ASN][1000 genomes]
rs2607631	0.94[ASN][1000 genomes]
rs2607632	0.91[ASN][1000 genomes]
rs2607633	0.89[ASN][1000 genomes]
rs2607635	0.85[ASN][1000 genomes]
rs2607636	0.91[ASN][1000 genomes]
rs2703377	0.88[ASN][1000 genomes]
rs2703382	0.82[ASN][1000 genomes]
rs2703384	0.85[ASN][1000 genomes]
rs2703386	0.89[ASN][1000 genomes]
rs2703387	0.88[ASN][1000 genomes]
rs2703388	0.81[ASN][1000 genomes]
rs2703389	0.88[ASN][1000 genomes]
rs2844231	0.89[ASN][1000 genomes]
rs2844234	0.83[ASN][1000 genomes]
rs2844235	0.83[ASN][1000 genomes]
rs2844236	0.83[ASN][1000 genomes]
rs2844254	0.91[ASN][1000 genomes]
rs2844255	0.91[ASN][1000 genomes]
rs2844256	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844257	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844258	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844259	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844260	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2844261	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808380	0.89[ASN][1000 genomes]
rs4529437	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6995356	0.95[ASN][1000 genomes]
rs7006166	0.98[ASN][1000 genomes]
rs7011340	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7011803	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs720139	0.97[ASN][1000 genomes]
rs720140	0.97[ASN][1000 genomes]
rs730885	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs753995	0.92[ASN][1000 genomes]
rs7818726	0.89[ASN][1000 genomes]
rs7821242	0.98[ASN][1000 genomes]
rs897840	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs897842	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs930877	0.91[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
rs10088684	PKHD1L1	cis	multi-tissue	Pritchard
rs10088684	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110543200-110550600	Weak transcription	GM12878-XiMat	blood
2	chr8:110543600-110551200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr8:110544400-110550800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr8:110545600-110551200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:110546600-110549600	Enhancers	Fetal Brain Male	brain
6	chr8:110546800-110548400	Enhancers	Fetal Brain Female	brain
7	chr8:110546800-110548600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:110546800-110549800	Enhancers	Fetal Lung	lung
9	chr8:110547200-110547800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:110547200-110548000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr8:110547200-110548000	Enhancers	NHEK	skin
12	chr8:110547200-110548200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr8:110547200-110548400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr8:110547400-110547800	Weak transcription	Brain Germinal Matrix	brain
15	chr8:110547400-110547800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr8:110547400-110548400	Enhancers	HSMM	muscle
17	chr8:110547400-110550600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr8:110547400-110550800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr8:110547400-110551200	Weak transcription	Fetal Intestine Small	intestine
20	chr8:110547600-110548400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr8:110547600-110548400	Enhancers	HSMMtube	muscle
22	chr8:110547600-110550600	Weak transcription	Rectal Mucosa Donor 29	rectum

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