Variant report

Variant	rs1042994
Chromosome Location	chr5:57751443-57751444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:57745705-57757136	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr5:57746016-57757149	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr5:57750892-57756934	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr5:57751391-57752625	SK-N-SH	brain:	n/a	n/a
5	SIN3AK20	chr5:57749882-57757124	MCF-7	breast:	n/a	n/a
6	POLR2A	chr5:57751357-57756911	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr5:57749894-57752638	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr5:57747447-57756979	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr5:57746933-57752694	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr5:57751348-57751629	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr5:57744593-57752591	A549	lung:	n/a	n/a
12	POLR2A	chr5:57751405-57752474	MCF-7	breast:	n/a	n/a
13	POLR2A	chr5:57749768-57756922	HUVEC	blood vessel:	n/a	n/a
14	CHD1	chr5:57751128-57757458	IMR90	lung:	n/a	n/a
15	POLR2A	chr5:57745515-57757046	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr5:57751337-57751701	Hela-S3	cervix:	n/a	n/a
17	GATA3	chr5:57746865-57752572	A549	lung:	n/a	chr5:57747131-57747148
18	POLR2A	chr5:57751305-57751621	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:57751319-57751626	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr5:57751300-57751620	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr5:57745756-57752683	PANC-1	pancreas:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:57751418-57751468	Hepatocyte	liver:	n/a
2	chr5:57751418-57751468	HAEpiC	amniotic membrane:	n/a
3	chr5:57751418-57751468	HPAEpiC	pulmonary alveolar:	n/a
4	chr5:57751418-57751468	NT2-D1	testis:	n/a
5	chr5:57751418-57751468	RPTEC	kidney:	n/a
6	chr5:57751418-57751468	PrEC	prostate:	n/a
7	chr5:57751418-57751468	HUVEC	blood vessel:	n/a
8	chr5:57751418-57751468	ovcar-3	ovarian:	n/a
9	chr5:57751418-57751468	ProgFib	skin:	n/a
10	chr5:57751418-57751468	NB4	blood:	n/a
11	chr5:57751418-57751468	A549	lung:	n/a
12	chr5:57751418-57751468	HRPEpiC	eye:	n/a
13	chr5:57751418-57751468	U87	brain:	n/a
14	chr5:57751418-57751468	Jurkat	blood:	n/a
15	chr5:57751418-57751468	Hela-S3	cervix:	n/a
16	chr5:57751418-57751468	HNPCEpiC	eye:	n/a
17	chr5:57751418-57751468	GM19239	blood:	n/a
18	chr5:57751418-57751468	NHDF-neo	bronchial:	n/a
19	chr5:57751418-57751468	HRCEpiC	kidney:	n/a
20	chr5:57751418-57751468	HCM	heart:	n/a
21	chr5:57751418-57751468	AG09319	gingival:	n/a
22	chr5:57751418-57751468	AoSMC	blood vessel:	n/a
23	chr5:57751418-57751468	HCPEpiC	choroid plexus:	n/a
24	chr5:57751418-57751468	HEEpiC	esophagus:	n/a
25	chr5:57751418-57751468	GM12878	blood:	n/a
26	chr5:57751418-57751468	PFSK-1	brain:	n/a
27	chr5:57751418-57751468	SK-N-MC	brain:	n/a
28	chr5:57751418-57751468	CMK	blood:	n/a
29	chr5:57751418-57751468	HEK293	kidney:	embryo
30	chr5:57751418-57751468	AG04449	skin:	fetal
31	chr5:57751418-57751468	H1-hESC	embryonic stem cell:	embryo
32	chr5:57751418-57751468	HepG2	liver:	n/a
33	chr5:57751418-57751468	PANC-1	pancreas:	n/a
34	chr5:57751418-57751468	BE2_C	brain:	n/a
35	chr5:57751418-57751468	GM12891	blood:	n/a
36	chr5:57751418-57751468	GM06990	blood:	n/a
37	chr5:57751418-57751468	AG09309	skin:	n/a
38	chr5:57751418-57751468	SAEC	small airway:	n/a
39	chr5:57751418-57751468	GM12892	blood:	n/a
40	chr5:57751418-57751468	SKMC	muscle:	n/a
41	chr5:57751418-57751468	NHBE	bronchial:	n/a
42	chr5:57751418-57751468	HL-60	blood:	n/a
43	chr5:57751418-57751468	BJ	skin:	n/a
44	chr5:57751418-57751468	SK-N-SH_RA	brain:	n/a
45	chr5:57751418-57751468	HCF	heart:	n/a
46	chr5:57751418-57751468	Caco-2	colon:	n/a
47	chr5:57751418-57751468	AG10803	skin:	n/a
48	chr5:57751418-57751468	MCF10A-Er-Src	breast:	n/a
49	chr5:57751418-57751468	LNCaP	prostate:	n/a
50	chr5:57751418-57751468	MCF-7	breast:	n/a

No data

Variant related genes	Relation type
PLK2	TF binding region
PLK2	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1035484	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1035485	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11546180	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12513877	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12513905	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12518781	0.85[AFR][1000 genomes]
rs12522386	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13168504	0.89[AFR][1000 genomes]
rs13184050	0.89[AFR][1000 genomes]
rs13188849	0.89[AFR][1000 genomes]
rs16888201	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17709855	0.94[YRI][hapmap];0.87[AFR][1000 genomes]
rs17710502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17710615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17767072	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2201293	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2220785	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2408946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2408947	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs33921924	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34150563	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34974449	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4699926	0.89[AFR][1000 genomes]
rs4700289	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs55827457	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56010771	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs56286824	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs56318521	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59135347	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62366360	0.87[AFR][1000 genomes]
rs6450474	0.86[AMR][1000 genomes]
rs6879330	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6882289	0.87[AFR][1000 genomes]
rs6890785	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72758162	0.93[EUR][1000 genomes]
rs72758173	0.82[AFR][1000 genomes]
rs7701530	0.89[AFR][1000 genomes]
rs7706545	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7708381	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7725097	0.82[AFR][1000 genomes]
rs7736949	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs929818	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1042994	GZMK	cis	cerebellum	SCAN
rs1042994	IPO11	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57747000-57752800	Weak transcription	Fetal Intestine Small	intestine
2	chr5:57747400-57752400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:57747800-57753000	Strong transcription	Liver	Liver
4	chr5:57747800-57754200	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:57748000-57752400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:57748400-57753400	Strong transcription	Fetal Intestine Large	intestine
7	chr5:57748600-57755000	Transcr. at gene 5' and 3'	A549	lung
8	chr5:57748800-57754200	Weak transcription	Primary B cells from cord blood	blood
9	chr5:57748800-57754600	Weak transcription	Spleen	Spleen
10	chr5:57749000-57754400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:57749200-57751800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:57749200-57752000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:57749200-57752400	Strong transcription	Placenta	Placenta
14	chr5:57749200-57752400	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:57749200-57753000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:57749200-57753400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
17	chr5:57749200-57754600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
18	chr5:57749200-57754800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
19	chr5:57749200-57755000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:57749200-57755000	Transcr. at gene 5' and 3'	NH-A	brain
21	chr5:57749400-57753200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:57749400-57753600	Genic enhancers	Fetal Heart	heart
23	chr5:57749600-57753000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:57749600-57753800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:57749600-57754800	Transcr. at gene 5' and 3'	HSMMtube	muscle
26	chr5:57749600-57755000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:57749800-57752200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:57749800-57754600	Transcr. at gene 5' and 3'	HMEC	breast
29	chr5:57750000-57752000	Genic enhancers	Adipose Nuclei	Adipose
30	chr5:57750000-57752600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:57750000-57753000	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr5:57750000-57753200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr5:57750000-57753200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
34	chr5:57750000-57754600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:57750000-57754600	Transcr. at gene 5' and 3'	NHEK	skin
36	chr5:57750000-57754800	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
37	chr5:57750000-57754800	Transcr. at gene 5' and 3'	HSMM	muscle
38	chr5:57750000-57754800	Transcr. at gene 5' and 3'	Osteobl	bone
39	chr5:57750000-57756800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:57750200-57751600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:57750200-57751600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:57750200-57751600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr5:57750200-57751600	Genic enhancers	Pancreas	Pancrea
44	chr5:57750200-57751800	Strong transcription	Fetal Stomach	stomach
45	chr5:57750200-57752000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:57750200-57752000	Genic enhancers	Esophagus	oesophagus
47	chr5:57750200-57752000	Transcr. at gene 5' and 3'	Pancreatic Islets	Pancreatic Islet
48	chr5:57750200-57752200	Genic enhancers	Small Intestine	intestine
49	chr5:57750200-57752400	Strong transcription	Dnd41	blood
50	chr5:57750200-57753000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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