Variant report

Variant	rs6469249
Chromosome Location	chr8:110237157-110237158
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:110234924..110237282-chr8:110242100..110245071,2	K562	blood:
2	chr8:110237132..110238315-chr8:110294080..110295100,5	MCF-7	breast:
3	chr8:110236599..110237927-chr8:110328052..110329074,4	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10087444	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10090944	0.84[ASN][1000 genomes]
rs10108349	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531298	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548082	0.86[JPT][hapmap]
rs1548083	0.86[JPT][hapmap]
rs1947629	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993594	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054257	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2125511	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125513	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2168964	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926195	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926196	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926197	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926198	0.87[JPT][hapmap]
rs2926201	0.81[ASN][1000 genomes]
rs2926208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926214	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926244	0.82[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2926245	0.87[JPT][hapmap]
rs2926247	0.86[JPT][hapmap]
rs2926259	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926263	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926265	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2926269	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2926277	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980565	0.86[JPT][hapmap]
rs2980589	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980591	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980602	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980603	0.87[JPT][hapmap]
rs2980606	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980611	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980618	0.82[JPT][hapmap]
rs2980619	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980620	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980621	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980623	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980624	0.87[JPT][hapmap]
rs2980627	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980628	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980630	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980632	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980636	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2980637	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2980639	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3116095	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3134105	0.91[YRI][hapmap]
rs4236802	0.84[YRI][hapmap]
rs4734194	0.85[ASN][1000 genomes]
rs4734195	0.85[ASN][1000 genomes]
rs4734206	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4734208	0.86[EUR][1000 genomes]
rs4735092	0.91[YRI][hapmap]
rs4735093	0.91[YRI][hapmap]
rs4735117	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4735119	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56247307	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6469235	0.84[ASN][1000 genomes]
rs6469241	0.86[ASN][1000 genomes]
rs6469248	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996836	0.83[ASN][1000 genomes]
rs7003376	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7003806	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7009169	0.92[ASN][1000 genomes]
rs7012304	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs720574	0.82[JPT][hapmap]
rs7819201	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7839867	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023204	chr8:110169573-110303085	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1031663	chr8:110177432-110303085	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv891272	chr8:110217266-110268104	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	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
5	nsv891274	chr8:110224047-110308776	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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
7	nsv891276	chr8:110232329-110308776	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6469249	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110191400-110237400	Weak transcription	Left Ventricle	heart
2	chr8:110211200-110311600	Weak transcription	Right Ventricle	heart
3	chr8:110225800-110241800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr8:110230400-110241000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:110231000-110238600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr8:110231800-110237400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:110231800-110242200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:110233600-110239000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr8:110233800-110237400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:110234200-110237400	Weak transcription	Pancreas	Pancrea
11	chr8:110234200-110241200	Weak transcription	HUVEC	blood vessel
12	chr8:110234400-110237400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr8:110234600-110237400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr8:110234600-110240400	Weak transcription	HMEC	breast
15	chr8:110234800-110238000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:110234800-110264200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr8:110235000-110237400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr8:110235000-110239000	Weak transcription	Liver	Liver
19	chr8:110235000-110239800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr8:110235000-110240600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr8:110235000-110251000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr8:110235200-110241400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:110235400-110237200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:110235400-110238600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:110235400-110271400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr8:110235400-110275000	Weak transcription	Fetal Brain Male	brain
27	chr8:110235600-110237800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr8:110235600-110244000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:110235800-110237200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr8:110235800-110238200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:110235800-110238200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr8:110235800-110238200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr8:110235800-110238200	ZNF genes & repeats	Fetal Muscle Leg	muscle
34	chr8:110235800-110239400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr8:110235800-110240400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:110235800-110241000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr8:110235800-110251200	Weak transcription	Fetal Intestine Large	intestine
38	chr8:110235800-110252600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr8:110236000-110237600	Strong transcription	A549	lung
40	chr8:110236000-110264200	Weak transcription	Spleen	Spleen
41	chr8:110236000-110265400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr8:110236200-110239000	Weak transcription	Dnd41	blood
43	chr8:110236200-110241000	Weak transcription	NH-A	brain
44	chr8:110236200-110244200	Weak transcription	Fetal Stomach	stomach
45	chr8:110236200-110264200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr8:110236200-110308800	Weak transcription	Thymus	Thymus
47	chr8:110236200-110309200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr8:110236400-110237600	Weak transcription	Fetal Lung	lung
49	chr8:110236400-110238200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
50	chr8:110236400-110240600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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