Variant report

Variant	rs62087456
Chromosome Location	chr18:9566437-9566438
allele	A/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	POLR2A	chr18:9566327-9566771	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9561179..9565835-chr18:9565855..9569697,6	K562	blood:
2	chr18:9551280..9553398-chr18:9564782..9567751,2	K562	blood:
3	chr18:9561179..9565835-chr18:9565855..9569697,5	K562	blood:

Variant related genes	Relation type
PPP4R1	TF binding region
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1036930	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081487	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12327541	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955297	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869737	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869738	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1869739	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028657	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365814	0.84[AMR][1000 genomes]
rs2840354	0.93[ASN][1000 genomes]
rs3786174	0.83[ASN][1000 genomes]
rs55841197	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56883068	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57539299	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58800301	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58982927	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59114729	0.83[ASN][1000 genomes]
rs59992205	0.83[ASN][1000 genomes]
rs60290408	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61166388	0.83[ASN][1000 genomes]
rs61275183	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62086146	0.83[ASN][1000 genomes]
rs62086147	0.83[ASN][1000 genomes]
rs62086151	0.83[ASN][1000 genomes]
rs62086152	0.83[ASN][1000 genomes]
rs62086155	0.83[ASN][1000 genomes]
rs62086156	0.83[ASN][1000 genomes]
rs62086158	0.83[ASN][1000 genomes]
rs62086159	0.83[ASN][1000 genomes]
rs62087363	0.83[ASN][1000 genomes]
rs62087368	0.83[ASN][1000 genomes]
rs62087370	0.83[ASN][1000 genomes]
rs62087371	0.83[ASN][1000 genomes]
rs62087378	0.83[ASN][1000 genomes]
rs62087402	0.83[ASN][1000 genomes]
rs62087403	0.83[ASN][1000 genomes]
rs62087404	0.83[ASN][1000 genomes]
rs62087406	0.83[ASN][1000 genomes]
rs62087407	0.83[ASN][1000 genomes]
rs62087411	0.83[ASN][1000 genomes]
rs62087412	0.83[ASN][1000 genomes]
rs62087414	0.83[ASN][1000 genomes]
rs62087415	0.83[ASN][1000 genomes]
rs62087416	0.83[ASN][1000 genomes]
rs62087417	0.80[ASN][1000 genomes]
rs62087427	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62088860	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088870	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088872	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088873	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088875	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088876	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088880	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088881	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088884	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088885	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088904	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088906	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088908	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6506677	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7228280	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231531	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7233308	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233649	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7234355	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235935	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7236274	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7237018	0.93[ASN][1000 genomes]
rs7238137	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7239083	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72945737	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732698	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73393880	0.83[ASN][1000 genomes]
rs73395717	0.83[ASN][1000 genomes]
rs73395719	0.83[ASN][1000 genomes]
rs8093600	0.88[AMR][1000 genomes]
rs8096551	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs894757	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9544000-9570200	Strong transcription	Fetal Intestine Large	intestine
2	chr18:9544000-9575600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr18:9544800-9572200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr18:9544800-9572400	Strong transcription	Primary T cells from cord blood	blood
5	chr18:9545200-9572600	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr18:9545800-9570200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr18:9545800-9583600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr18:9545800-9595200	Strong transcription	Dnd41	blood
9	chr18:9549600-9581800	Weak transcription	Psoas Muscle	Psoas
10	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr18:9553000-9572400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr18:9553000-9573000	Strong transcription	Fetal Muscle Leg	muscle
13	chr18:9553000-9573600	Strong transcription	NHDF-Ad	bronchial
14	chr18:9553200-9572600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr18:9553200-9575800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr18:9553800-9572800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr18:9553800-9573000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr18:9553800-9574600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr18:9553800-9582000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr18:9554000-9574000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr18:9554000-9574200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr18:9554000-9576000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr18:9554400-9578400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr18:9555400-9580600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr18:9557800-9575800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr18:9558000-9580600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:9558400-9570600	Strong transcription	HUVEC	blood vessel
29	chr18:9559000-9586800	Weak transcription	Small Intestine	intestine
30	chr18:9559600-9570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr18:9559600-9570200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr18:9559600-9571600	Weak transcription	Fetal Brain Male	brain
33	chr18:9559600-9580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr18:9559600-9587000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr18:9559800-9569400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr18:9560200-9575200	Weak transcription	Stomach Mucosa	stomach
37	chr18:9560200-9577600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr18:9560400-9577600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:9561000-9575800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr18:9562000-9574000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr18:9563000-9569000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr18:9563000-9569800	Weak transcription	Pancreas	Pancrea
43	chr18:9563000-9570200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr18:9563000-9581600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr18:9563200-9567400	Weak transcription	A549	lung
46	chr18:9563200-9580600	Weak transcription	Aorta	Aorta
47	chr18:9563400-9567400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr18:9563400-9567800	Weak transcription	GM12878-XiMat	blood
49	chr18:9563400-9571400	Weak transcription	Fetal Kidney	kidney
50	chr18:9563600-9567200	Weak transcription	Brain Cingulate Gyrus	brain

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