Variant report

Variant	rs62088882
Chromosome Location	chr18:9602027-9602028
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	RFX5	chr18:9601976-9602144	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9574087..9576896-chr18:9600490..9602058,2	K562	blood:
2	chr18:9584735..9586577-chr18:9599877..9602634,2	K562	blood:
3	chr18:9580227..9582159-chr18:9599784..9602426,2	K562	blood:

Variant related genes	Relation type
PPP4R1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs61746389	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61749090	0.85[EUR][1000 genomes]
rs61749091	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62080294	0.85[AMR][1000 genomes]
rs62080298	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62080299	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62080302	0.81[EUR][1000 genomes]
rs62080303	0.81[EUR][1000 genomes]
rs62087423	0.80[EUR][1000 genomes]
rs62087424	0.97[EUR][1000 genomes]
rs62087455	0.97[EUR][1000 genomes]
rs62087457	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62087458	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62088862	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62088863	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62088865	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62088866	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62088867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62088869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62088874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62088909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62088910	0.95[AMR][1000 genomes]
rs62088911	0.83[EUR][1000 genomes]
rs62088912	0.81[EUR][1000 genomes]
rs62088913	0.81[EUR][1000 genomes]
rs62088914	0.81[EUR][1000 genomes]
rs62088915	0.85[EUR][1000 genomes]
rs62088917	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62088918	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7236182	0.81[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62088882	RP11-692N5.1	cis	Esophagus Mucosa	GTEx
rs62088882	RALBP1	cis	Whole Blood	GTEx

Chromatin state (count:60 , 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	chr18:9581400-9609200	Weak transcription	Pancreas	Pancrea
4	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr18:9589000-9608800	Weak transcription	Thymus	Thymus
6	chr18:9589000-9609200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr18:9589000-9611000	Weak transcription	Lung	lung
8	chr18:9594200-9609200	Weak transcription	Aorta	Aorta
9	chr18:9594200-9613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr18:9595200-9612000	Weak transcription	Esophagus	oesophagus
11	chr18:9595400-9608800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr18:9596000-9605800	Weak transcription	Hela-S3	cervix
13	chr18:9596000-9611000	Weak transcription	Gastric	stomach
14	chr18:9597000-9603200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:9597000-9608800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr18:9597200-9604200	Weak transcription	Left Ventricle	heart
17	chr18:9597200-9611000	Weak transcription	NH-A	brain
18	chr18:9597400-9604600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr18:9597400-9608000	Weak transcription	Osteobl	bone
20	chr18:9597400-9609200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr18:9597400-9613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr18:9597600-9606000	Weak transcription	HUVEC	blood vessel
23	chr18:9597600-9609200	Weak transcription	Ovary	ovary
24	chr18:9597800-9603400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:9598000-9604400	Weak transcription	HMEC	breast
26	chr18:9598000-9612600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr18:9598800-9602200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr18:9600200-9604600	Weak transcription	HepG2	liver
29	chr18:9600200-9609400	Weak transcription	HSMM	muscle
30	chr18:9600600-9602800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr18:9600800-9603800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr18:9600800-9604200	Weak transcription	Psoas Muscle	Psoas
33	chr18:9600800-9608400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr18:9601000-9602200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr18:9601000-9605800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr18:9601000-9608200	Weak transcription	Stomach Mucosa	stomach
37	chr18:9601200-9604400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr18:9601200-9604400	Weak transcription	NHEK	skin
39	chr18:9601200-9608200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr18:9601200-9608400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr18:9601200-9608400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr18:9601400-9604200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr18:9601400-9604400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr18:9601400-9605400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr18:9601400-9608200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr18:9601400-9608200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr18:9601400-9608400	Weak transcription	NHLF	lung
48	chr18:9601400-9609200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr18:9601400-9610800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr18:9601600-9608200	Weak transcription	Fetal Intestine Small	intestine

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