Variant report

Variant	rs62088875
Chromosome Location	chr18:9597529-9597530
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	SETDB1	chr18:9597396-9598206	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9594858..9597558-chr18:9614248..9616397,2	MCF-7	breast:
2	chr18:9581775..9584005-chr18:9596096..9598190,2	K562	blood:
3	chr18:9595087..9597869-chr18:9607007..9610720,3	MCF-7	breast:
4	chr18:9596087..9600746-chr18:9613522..9617540,6	MCF-7	breast:
5	chr18:9593612..9595267-chr18:9595493..9597647,2	K562	blood:

Variant related genes	Relation type
PPP4R1	TF binding region
ENSG00000154845	Chromatin interaction
ENSG00000263627	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1036930	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081487	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12327541	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955297	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869737	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869738	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1869739	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028657	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840354	0.93[ASN][1000 genomes]
rs3786174	0.83[ASN][1000 genomes]
rs55841197	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56883068	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57539299	0.93[ASN][1000 genomes]
rs58800301	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58982927	0.93[ASN][1000 genomes]
rs59114729	0.83[ASN][1000 genomes]
rs59992205	0.83[ASN][1000 genomes]
rs60290408	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61166388	0.83[ASN][1000 genomes]
rs61275183	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62087456	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088860	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088870	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088872	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088873	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088876	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088880	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088881	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088884	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088885	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088904	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088906	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088908	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6506677	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7228280	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231531	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7233308	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233649	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7234355	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235935	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7236274	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7237018	0.93[ASN][1000 genomes]
rs7238137	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7239083	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72945737	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732698	0.86[AMR][1000 genomes];0.97[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]
rs8096551	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs894757	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:9576200-9597800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:9581400-9609200	Weak transcription	Pancreas	Pancrea
5	chr18:9582800-9597600	Weak transcription	Fetal Brain Male	brain
6	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr18:9589000-9608800	Weak transcription	Thymus	Thymus
8	chr18:9589000-9609200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr18:9589000-9611000	Weak transcription	Lung	lung
10	chr18:9589200-9598200	Weak transcription	Primary B cells from cord blood	blood
11	chr18:9589200-9599200	Weak transcription	Fetal Kidney	kidney
12	chr18:9590800-9597600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr18:9592400-9599400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr18:9592600-9599800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr18:9593000-9598800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr18:9594000-9597600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr18:9594000-9599400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr18:9594200-9600400	Weak transcription	Placenta	Placenta
19	chr18:9594200-9600400	Weak transcription	Fetal Stomach	stomach
20	chr18:9594200-9600600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:9594200-9609200	Weak transcription	Aorta	Aorta
22	chr18:9594200-9613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr18:9594400-9600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr18:9594800-9597600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr18:9594800-9597800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr18:9594800-9600200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr18:9594800-9600400	Weak transcription	Fetal Thymus	thymus
28	chr18:9595000-9597600	Enhancers	HUVEC	blood vessel
29	chr18:9595000-9597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr18:9595200-9598000	Weak transcription	Dnd41	blood
31	chr18:9595200-9599600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr18:9595200-9612000	Weak transcription	Esophagus	oesophagus
33	chr18:9595400-9599400	Weak transcription	Brain Hippocampus Middle	brain
34	chr18:9595400-9601800	Weak transcription	Fetal Heart	heart
35	chr18:9595400-9608800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr18:9595600-9598000	Enhancers	HMEC	breast
37	chr18:9595600-9600600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr18:9595800-9599800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr18:9596000-9597800	Enhancers	NHEK	skin
40	chr18:9596000-9598000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr18:9596000-9605800	Weak transcription	Hela-S3	cervix
42	chr18:9596000-9611000	Weak transcription	Gastric	stomach
43	chr18:9596600-9599200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr18:9597000-9597600	Enhancers	HepG2	liver
45	chr18:9597000-9597800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
46	chr18:9597000-9598400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr18:9597000-9599000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr18:9597000-9599200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:9597000-9600000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr18:9597000-9601400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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