Variant report

Variant	rs13249244
Chromosome Location	chr8:110550381-110550382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:110532017..110535509-chr8:110550359..110553902,4	K562	blood:
2	chr8:110550248..110554482-chr8:110655662..110659384,5	MCF-7	breast:
3	chr8:110480733..110484366-chr8:110549857..110553138,3	MCF-7	breast:
4	chr8:110532422..110535509-chr8:110550359..110553902,3	K562	blood:
5	chr8:110491337..110493958-chr8:110550109..110551629,2	MCF-7	breast:
6	chr8:110356416..110359294-chr8:110548274..110550933,2	MCF-7	breast:
7	chr8:110344871..110348245-chr8:110549404..110554651,7	MCF-7	breast:
8	chr8:110490813..110493110-chr8:110549363..110552380,3	MCF-7	breast:
9	chr8:110549295..110551335-chr8:110575398..110578462,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000147642	Chromatin interaction
ENSG00000120526	Chromatin interaction
ENSG00000205038	Chromatin interaction
ENSG00000254185	Chromatin interaction
ENSG00000120533	Chromatin interaction
ENSG00000248050	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10088258	0.95[ASN][1000 genomes]
rs10088612	0.98[ASN][1000 genomes]
rs10088684	0.98[ASN][1000 genomes]
rs1009371	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10108943	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111682	0.95[ASN][1000 genomes]
rs1013482	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1026437	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1044230	0.88[ASN][1000 genomes]
rs10505133	0.98[ASN][1000 genomes]
rs13439318	0.98[ASN][1000 genomes]
rs13439864	0.98[ASN][1000 genomes]
rs1379361	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1379366	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1379367	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1457282	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1457283	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1457288	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1457294	0.97[ASN][1000 genomes]
rs1457295	0.97[ASN][1000 genomes]
rs1563578	0.97[ASN][1000 genomes]
rs1563580	0.91[ASN][1000 genomes]
rs1617259	0.98[ASN][1000 genomes]
rs1617350	0.98[ASN][1000 genomes]
rs1630134	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1630942	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1673383	0.98[ASN][1000 genomes]
rs1673384	0.98[ASN][1000 genomes]
rs1673386	0.95[ASN][1000 genomes]
rs1673389	0.98[ASN][1000 genomes]
rs1673395	0.98[ASN][1000 genomes]
rs1673399	0.98[ASN][1000 genomes]
rs1673409	0.97[ASN][1000 genomes]
rs1673410	0.97[ASN][1000 genomes]
rs1673411	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673413	0.97[ASN][1000 genomes]
rs1673415	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673416	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673419	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673420	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673421	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1673424	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673425	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673426	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673427	0.97[ASN][1000 genomes]
rs1673428	0.97[ASN][1000 genomes]
rs17377636	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17449762	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783140	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1783147	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1783148	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1783153	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783154	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783155	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783157	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783158	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1783159	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1783161	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783162	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783166	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783167	0.97[ASN][1000 genomes]
rs1783168	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783169	0.94[ASN][1000 genomes]
rs1783170	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783171	0.97[ASN][1000 genomes]
rs1783172	0.97[ASN][1000 genomes]
rs1783173	0.94[ASN][1000 genomes]
rs1783174	0.97[ASN][1000 genomes]
rs1783175	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892760	0.81[ASN][1000 genomes]
rs2022934	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2022935	0.95[ASN][1000 genomes]
rs2154660	0.98[ASN][1000 genomes]
rs2236627	0.82[ASN][1000 genomes]
rs2236628	0.81[ASN][1000 genomes]
rs2607624	0.97[ASN][1000 genomes]
rs2607625	0.97[ASN][1000 genomes]
rs2607627	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607628	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607629	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607630	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607631	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607632	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2607633	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2607635	0.84[ASN][1000 genomes]
rs2607636	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2703377	0.88[ASN][1000 genomes]
rs2703382	0.81[ASN][1000 genomes]
rs2703384	0.85[ASN][1000 genomes]
rs2703386	0.91[ASN][1000 genomes]
rs2703387	0.88[ASN][1000 genomes]
rs2703389	0.88[ASN][1000 genomes]
rs2844231	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844234	0.82[ASN][1000 genomes]
rs2844235	0.81[ASN][1000 genomes]
rs2844236	0.81[ASN][1000 genomes]
rs2844254	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2844255	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2844256	0.92[ASN][1000 genomes]
rs2844257	0.97[ASN][1000 genomes]
rs2844258	0.97[ASN][1000 genomes]
rs2844259	0.96[ASN][1000 genomes]
rs2844260	0.94[ASN][1000 genomes]
rs2844261	0.97[ASN][1000 genomes]
rs3808380	0.89[ASN][1000 genomes]
rs4529437	0.95[ASN][1000 genomes]
rs6995356	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7006166	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7011340	0.98[ASN][1000 genomes]
rs7011803	0.95[ASN][1000 genomes]
rs720139	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs720140	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs730885	0.94[ASN][1000 genomes]
rs753995	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7818726	0.90[ASN][1000 genomes]
rs7821242	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897840	0.97[ASN][1000 genomes]
rs897842	0.97[ASN][1000 genomes]
rs930877	0.89[EUR][1000 genomes];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
rs13249244	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs13249244	PKHD1L1	cis	multi-tissue	Pritchard

Chromatin state (count:39 , 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	chr8:110547400-110550600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr8:110547400-110550800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr8:110547400-110551200	Weak transcription	Fetal Intestine Small	intestine
8	chr8:110547600-110550600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr8:110547800-110551000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:110548000-110551200	Weak transcription	NHEK	skin
11	chr8:110548200-110551000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr8:110548200-110551000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr8:110548200-110551000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr8:110548200-110551000	Weak transcription	Hela-S3	cervix
15	chr8:110548400-110550600	Weak transcription	Fetal Brain Female	brain
16	chr8:110548400-110550800	Weak transcription	Colonic Mucosa	Colon
17	chr8:110548400-110551000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr8:110548400-110551000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr8:110548400-110551200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr8:110548400-110551200	Weak transcription	HSMMtube	muscle
21	chr8:110548600-110551200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr8:110549600-110550800	Weak transcription	Fetal Brain Male	brain
23	chr8:110549600-110551000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr8:110549600-110551000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr8:110549600-110551000	Enhancers	Brain Germinal Matrix	brain
26	chr8:110549600-110551400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr8:110549800-110550800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr8:110549800-110550800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr8:110549800-110550800	Weak transcription	Fetal Lung	lung
30	chr8:110549800-110551000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr8:110549800-110551000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr8:110549800-110551000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr8:110549800-110551200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr8:110549800-110551200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr8:110550000-110550400	Weak transcription	K562	blood
36	chr8:110550000-110550800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:110550000-110551000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr8:110550200-110550600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr8:110550200-110550600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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