Variant report

Variant	rs2168964
Chromosome Location	chr8:110311638-110311639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10087444	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10108349	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1380096	0.87[JPT][hapmap]
rs1380097	0.87[JPT][hapmap]
rs1458915	0.87[JPT][hapmap]
rs1458916	0.87[JPT][hapmap]
rs1458917	0.87[JPT][hapmap]
rs1458923	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1531298	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1548082	0.86[JPT][hapmap]
rs1548083	0.87[JPT][hapmap]
rs1947629	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1993594	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054257	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2125511	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2125513	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2926195	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926196	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926197	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926198	0.87[JPT][hapmap]
rs2926208	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926214	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926244	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2926245	0.87[JPT][hapmap]
rs2926247	0.87[JPT][hapmap]
rs2926259	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926263	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926269	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2926277	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980565	0.87[JPT][hapmap]
rs2980589	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980591	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980602	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2980603	0.87[JPT][hapmap]
rs2980606	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2980611	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980614	0.81[ASN][1000 genomes]
rs2980618	0.82[JPT][hapmap]
rs2980619	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980620	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980621	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980623	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];0.99[ASN][1000 genomes]
rs2980624	0.87[JPT][hapmap]
rs2980627	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980628	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980630	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980632	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980636	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980637	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980639	0.81[JPT][hapmap]
rs3116095	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4236802	0.84[YRI][hapmap]
rs4734206	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4734208	0.86[EUR][1000 genomes]
rs4735092	0.92[YRI][hapmap]
rs4735093	0.84[YRI][hapmap]
rs4735117	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4735119	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56247307	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6469241	0.81[ASN][1000 genomes]
rs6469248	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6469249	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7003376	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7003806	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7009169	0.87[ASN][1000 genomes]
rs7012304	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs720574	0.83[JPT][hapmap]
rs7819201	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7839867	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891273	chr8:110219735-110475874	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv891275	chr8:110224047-110319234	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv891279	chr8:110268104-110450092	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2168964	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110236600-110344200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:110284400-110344400	Weak transcription	Fetal Lung	lung
3	chr8:110288200-110311800	Weak transcription	K562	blood
4	chr8:110288600-110344200	Weak transcription	Ovary	ovary
5	chr8:110292000-110333200	Weak transcription	HepG2	liver
6	chr8:110293000-110343600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr8:110294600-110314600	Weak transcription	Pancreas	Pancrea
8	chr8:110302600-110312000	Weak transcription	Placenta	Placenta
9	chr8:110303000-110313200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr8:110304600-110313200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:110305200-110318200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr8:110305600-110317800	Weak transcription	Osteobl	bone
13	chr8:110305600-110318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr8:110306200-110312200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr8:110306200-110314000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr8:110306200-110316600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr8:110306400-110312400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr8:110306600-110324800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr8:110307200-110311800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr8:110307200-110314000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr8:110307600-110333000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr8:110307800-110317200	Weak transcription	Primary B cells from cord blood	blood
23	chr8:110309200-110311800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr8:110309200-110311800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr8:110309200-110312400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr8:110309200-110321200	Weak transcription	Thymus	Thymus
27	chr8:110309400-110312000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr8:110309400-110314400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr8:110310600-110312400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr8:110311000-110311800	ZNF genes & repeats	Fetal Intestine Large	intestine
31	chr8:110311000-110312200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:110311000-110312200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr8:110311000-110312400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr8:110311200-110311800	Enhancers	Esophagus	oesophagus
35	chr8:110311200-110312000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr8:110311200-110312000	Enhancers	Fetal Muscle Trunk	muscle
37	chr8:110311200-110312000	Enhancers	Gastric	stomach
38	chr8:110311200-110312200	Enhancers	H1 Cell Line	embryonic stem cell
39	chr8:110311200-110312200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr8:110311200-110312200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr8:110311200-110312200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr8:110311200-110312200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr8:110311200-110312200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:110311200-110312200	Enhancers	Lung	lung
45	chr8:110311200-110312200	Enhancers	A549	lung
46	chr8:110311200-110312400	Enhancers	H9 Cell Line	embryonic stem cell
47	chr8:110311200-110312400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr8:110311400-110311800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr8:110311400-110311800	Enhancers	Small Intestine	intestine
50	chr8:110311400-110312000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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