Variant report

Variant	rs5030539
Chromosome Location	chr4:110621820-110621821
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	CTCF	chr4:110621820-110621970	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr4:110621820-110621970	HCT-116	colon:	n/a	n/a
3	CTCF	chr4:110621820-110622110	RPTEC	kidney:	n/a	chr4:110622066-110622084 chr4:110622068-110622089 chr4:110622069-110622082 chr4:110622067-110622083
4	CTCF	chr4:110621820-110621970	NHDF-neo	bronchial:	n/a	n/a
5	CTCF	chr4:110621820-110621970	BJ	skin:	n/a	n/a
6	CTCF	chr4:110621800-110621950	GM12873	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:110620445..110623344-chr4:110627846..110630459,3	K562	blood:
2	chr4:110621753..110625851-chr4:110723328..110725382,3	MCF-7	breast:
3	chr4:110614175..110617352-chr4:110621711..110624911,3	K562	blood:
4	chr4:110621463..110624410-chr4:110832783..110835223,2	K562	blood:
5	chr4:110609534..110611463-chr4:110619713..110622437,2	K562	blood:
6	chr4:110618563..110622220-chr4:110622548..110625878,6	K562	blood:
7	chr4:110621787..110624443-chr4:110734368..110736643,3	K562	blood:
8	chr4:110611670..110613762-chr4:110619125..110621842,2	K562	blood:

Variant related genes	Relation type
CASP6	TF binding region
ENSG00000138798	Chromatin interaction
ENSG00000205403	Chromatin interaction
ENSG00000273447	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000138794	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10004377	0.92[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11728699	0.85[CEU][hapmap]
rs11932526	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13107296	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13127878	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1541373	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17512351	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2237056	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301717	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3087494	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3181187	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5030534	0.84[EUR][1000 genomes]
rs5030535	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6533448	0.99[ASN][1000 genomes]
rs6533449	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6533451	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6812043	0.99[ASN][1000 genomes]
rs6831917	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6854876	0.82[CEU][hapmap]
rs7439493	0.80[CEU][hapmap]
rs7674356	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7682236	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7694620	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9992400	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9995011	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5030539	PLA2G12A	cis	brain	BrainEAC
rs5030539	LARP7	cis	parietal	SCAN
rs5030539	CASP6	cis	parietal	SCAN
rs5030539	RRH	cis	cerebellum	SCAN
rs5030539	CASP6	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
2	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
3	chr4:110598800-110622800	Weak transcription	NHEK	skin
4	chr4:110600800-110622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:110601800-110622800	Weak transcription	Right Atrium	heart
6	chr4:110605000-110622800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:110605600-110622800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:110605800-110622800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:110606400-110622800	Weak transcription	Hela-S3	cervix
10	chr4:110607200-110622800	Weak transcription	Fetal Brain Male	brain
11	chr4:110607800-110623200	Weak transcription	Brain Angular Gyrus	brain
12	chr4:110609000-110622800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:110609600-110623000	Weak transcription	A549	lung
14	chr4:110609800-110623200	Weak transcription	Psoas Muscle	Psoas
15	chr4:110611000-110623200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:110611200-110623800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:110611600-110622600	Weak transcription	Fetal Heart	heart
18	chr4:110611600-110623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:110612200-110622800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:110612200-110623000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:110612400-110622800	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:110613000-110623200	Weak transcription	Brain Anterior Caudate	brain
23	chr4:110613200-110622400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:110613600-110622800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:110613800-110622800	Weak transcription	NHDF-Ad	bronchial
26	chr4:110614200-110622600	Weak transcription	Brain Germinal Matrix	brain
27	chr4:110614200-110622800	Weak transcription	Right Ventricle	heart
28	chr4:110614200-110622800	Weak transcription	HMEC	breast
29	chr4:110614200-110623000	Weak transcription	NHLF	lung
30	chr4:110614200-110623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:110614400-110622800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr4:110614400-110622800	Weak transcription	Primary B cells from cord blood	blood
33	chr4:110614400-110622800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr4:110614400-110622800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:110614400-110622800	Weak transcription	Ovary	ovary
36	chr4:110614400-110622800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:110614400-110623000	Weak transcription	NH-A	brain
38	chr4:110614600-110622600	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:110614600-110622800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr4:110615400-110622800	Weak transcription	Placenta	Placenta
41	chr4:110615400-110623200	Weak transcription	Aorta	Aorta
42	chr4:110615600-110622600	Weak transcription	Spleen	Spleen
43	chr4:110615600-110623000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:110615800-110622600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:110615800-110622600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:110615800-110622600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:110615800-110622800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:110615800-110623000	Weak transcription	Fetal Kidney	kidney
49	chr4:110615800-110623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:110616000-110622600	Weak transcription	Primary monocytes fromperipheralblood	blood

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