Variant report

Variant	rs1059227
Chromosome Location	chr6:36098410-36098411
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:72)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:72 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:36097665-36098499	MCF10A-Er-Src	breast:	n/a	n/a
2	TAF1	chr6:36097873-36099372	HepG2	liver:	n/a	n/a
3	ZBTB7A	chr6:36097829-36098527	ECC-1	luminal epithelium:	n/a	n/a
4	PML	chr6:36097789-36099232	GM12878	blood:	n/a	n/a
5	HEY1	chr6:36098067-36098481	HepG2	liver:	n/a	n/a
6	MAX	chr6:36097928-36099394	H1-hESC	embryonic stem cell:	n/a	n/a
7	TBP	chr6:36098313-36099869	HepG2	liver:	n/a	n/a
8	MXI1	chr6:36098009-36099935	HepG2	liver:	n/a	chr6:36099510-36099519
9	MXI1	chr6:36098347-36099977	GM12878	blood:	n/a	chr6:36099510-36099519
10	POLR2A	chr6:36098307-36099151	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr6:36097896-36099361	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:36098011-36099232	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:36098275-36099121	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr6:36097848-36098484	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr6:36097815-36098477	HepG2	liver:	n/a	n/a
16	RUNX3	chr6:36098358-36100003	GM12878	blood:	n/a	chr6:36098575-36098590
17	POLR2A	chr6:36097833-36099850	HepG2	liver:	n/a	n/a
18	EBF1	chr6:36098379-36098790	GM12878	blood:	n/a	chr6:36098657-36098668
19	FOXA2	chr6:36098282-36098464	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:36097730-36099330	HCT-116	colon:	n/a	n/a
21	ZBTB7A	chr6:36098277-36098804	HepG2	liver:	n/a	chr6:36098565-36098574
22	TCF7L2	chr6:36097984-36098811	HCT-116	colon:	n/a	n/a
23	E2F6	chr6:36097863-36098439	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr6:36098374-36099234	H1-hESC	embryonic stem cell:	n/a	chr6:36098618-36098630 chr6:36098620-36098628
25	POLR2A	chr6:36098385-36098924	GM12878	blood:	n/a	n/a
26	FOXA1	chr6:36098134-36098887	HepG2	liver:	n/a	n/a
27	CTCF	chr6:36098400-36098550	GM12875	blood:	n/a	n/a
28	MAX	chr6:36097866-36100302	MCF-7	breast:	n/a	n/a
29	ZBTB7A	chr6:36098315-36098654	HepG2	liver:	n/a	chr6:36098565-36098574
30	POLR2A	chr6:36097829-36099147	HCT-116	colon:	n/a	n/a
31	POLR2A	chr6:36098000-36099863	GM15510	blood:	n/a	n/a
32	ZEB1	chr6:36097826-36098517	GM12878	blood:	n/a	chr6:36098189-36098198 chr6:36098190-36098201
33	POLR2A	chr6:36097890-36098470	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr6:36097835-36100139	HepG2	liver:	n/a	n/a
35	HEY1	chr6:36097516-36099900	HepG2	liver:	n/a	chr6:36098036-36098051
36	POLR2A	chr6:36098369-36099880	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:36098279-36099680	HepG2	liver:	n/a	n/a
38	MAX	chr6:36097803-36100303	HepG2	liver:	n/a	n/a
39	NFIC	chr6:36098253-36098897	HepG2	liver:	n/a	n/a
40	MAZ	chr6:36098087-36099631	HepG2	liver:	n/a	n/a
41	YY1	chr6:36098180-36098755	GM12878	blood:	n/a	chr6:36098618-36098630 chr6:36098334-36098345 chr6:36098620-36098628
42	MAZ	chr6:36098035-36099854	GM12878	blood:	n/a	n/a
43	HDAC2	chr6:36097789-36098878	HepG2	liver:	n/a	n/a
44	POLR2A	chr6:36097614-36099831	HCT-116	colon:	n/a	n/a
45	POLR2A	chr6:36097970-36100007	HepG2	liver:	n/a	n/a
46	EP300	chr6:36098386-36099132	HepG2	liver:	n/a	n/a
47	TCF12	chr6:36097926-36098550	ECC-1	luminal epithelium:	n/a	chr6:36098108-36098115
48	POLR2A	chr6:36097929-36098876	MCF-7	breast:	n/a	n/a
49	POLR2A	chr6:36097605-36098447	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr6:36098242-36098478	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:36098398-36098448	GM06990	blood:	n/a
2	chr6:36098398-36098448	A549	lung:	n/a
3	chr6:36098398-36098448	HRE	kidney:	n/a
4	chr6:36098398-36098448	NT2-D1	testis:	n/a
5	chr6:36098398-36098448	NHDF-neo	bronchial:	n/a
6	chr6:36098398-36098448	RPTEC	kidney:	n/a
7	chr6:36098398-36098448	HMEC	breast:	n/a
8	chr6:36098398-36098448	NH-A	brain:	n/a
9	chr6:36098398-36098448	HL-60	blood:	n/a
10	chr6:36098398-36098448	BJ	skin:	n/a
11	chr6:36098398-36098448	HEK293	kidney:	embryo
12	chr6:36098398-36098448	AG04449	skin:	fetal
13	chr6:36098398-36098448	HEEpiC	esophagus:	n/a
14	chr6:36098398-36098448	NB4	blood:	n/a
15	chr6:36098398-36098448	HCF	heart:	n/a
16	chr6:36098398-36098448	HCM	heart:	n/a
17	chr6:36098398-36098448	HRCEpiC	kidney:	n/a
18	chr6:36098398-36098448	HCPEpiC	choroid plexus:	n/a
19	chr6:36098398-36098448	SK-N-SH_RA	brain:	n/a
20	chr6:36098398-36098448	HRPEpiC	eye:	n/a
21	chr6:36098398-36098448	Hela-S3	cervix:	n/a
22	chr6:36098398-36098448	SAEC	small airway:	n/a
23	chr6:36098398-36098448	HepG2	liver:	n/a
24	chr6:36098398-36098448	U87	brain:	n/a
25	chr6:36098398-36098448	GM12892	blood:	n/a
26	chr6:36098398-36098448	CMK	blood:	n/a
27	chr6:36098398-36098448	ovcar-3	ovarian:	n/a
28	chr6:36098398-36098448	AG10803	skin:	n/a
29	chr6:36098398-36098448	NHBE	bronchial:	n/a
30	chr6:36098398-36098448	AG09309	skin:	n/a
31	chr6:36098398-36098448	SK-N-MC	brain:	n/a
32	chr6:36098398-36098448	PANC-1	pancreas:	n/a
33	chr6:36098398-36098448	SK-N-SH	brain:	n/a
34	chr6:36098398-36098448	PFSK-1	brain:	n/a
35	chr6:36098398-36098448	HNPCEpiC	eye:	n/a
36	chr6:36098398-36098448	HUVEC	blood vessel:	n/a
37	chr6:36098398-36098448	Jurkat	blood:	n/a
38	chr6:36098398-36098448	GM12891	blood:	n/a
39	chr6:36098398-36098448	HIPEpiC	eye:	n/a
40	chr6:36098398-36098448	IMR90	lung:	fetal
41	chr6:36098398-36098448	HAEpiC	amniotic membrane:	n/a
42	chr6:36098398-36098448	GM19239	blood:	n/a
43	chr6:36098398-36098448	T-47D	breast:	n/a
44	chr6:36098398-36098448	ECC-1	luminal epithelium:	n/a
45	chr6:36098398-36098448	AG09319	gingival:	n/a
46	chr6:36098398-36098448	Hepatocyte	liver:	n/a
47	chr6:36098398-36098448	SKMC	muscle:	n/a
48	chr6:36098398-36098448	PrEC	prostate:	n/a
49	chr6:36098398-36098448	MCF-7	breast:	n/a
50	chr6:36098398-36098448	AG04450	lung:	fetal

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36097672..36103046-chr6:36163327..36166048,5	MCF-7	breast:
2	chr6:36097129..36099054-chr6:36162391..36164603,2	K562	blood:
3	chr6:36098131..36102554-chr6:36163258..36166179,4	K562	blood:
4	chr6:36096617..36099142-chr6:36162886..36164936,2	MCF-7	breast:

No data

Variant related genes	Relation type
MAPK13	TF binding region
MAPK13	CpG island
ENSG00000246982	Chromatin interaction
ENSG00000096070	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10447375	0.84[AMR][1000 genomes]
rs10447396	0.86[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10947589	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12193895	0.85[ASN][1000 genomes]
rs12199702	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs12201072	0.85[ASN][1000 genomes]
rs12210904	0.88[AMR][1000 genomes]
rs12210946	0.83[ASN][1000 genomes]
rs12525283	1.00[JPT][hapmap]
rs17715809	1.00[JPT][hapmap]
rs2007683	0.93[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859135	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2859136	0.86[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2859137	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2859141	0.93[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711433	0.85[AMR][1000 genomes]
rs6940723	0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1059227	MAPK13	cis	parietal	SCAN
rs1059227	MAPK13	cis	Skin Sun Exposed Lower leg	GTEx
rs1059227	MAPK13	Cis_1M	lymphoblastoid	RTeQTL
rs1059227	MAPK13	cis	Esophagus Mucosa	GTEx
rs1059227	SCUBE3	cis	cerebellum	SCAN
rs1059227	CLPS	cis	parietal	SCAN
rs1059227	KIF6	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36095600-36099000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:36096200-36099200	Weak transcription	HSMM	muscle
3	chr6:36096400-36099200	Weak transcription	K562	blood
4	chr6:36096600-36099200	Weak transcription	Hela-S3	cervix
5	chr6:36097400-36099800	Enhancers	HUVEC	blood vessel
6	chr6:36097600-36098600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr6:36097600-36098600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:36097600-36098600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:36097600-36098600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr6:36097600-36098600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:36097600-36098600	Active TSS	Pancreas	Pancrea
12	chr6:36097600-36099000	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr6:36097600-36099400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:36097600-36099800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:36097600-36100200	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr6:36097600-36101000	Enhancers	Fetal Heart	heart
17	chr6:36097800-36098600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:36097800-36098600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
19	chr6:36097800-36098600	Active TSS	Esophagus	oesophagus
20	chr6:36097800-36098600	Bivalent/Poised TSS	Fetal Stomach	stomach
21	chr6:36097800-36098600	Bivalent/Poised TSS	Psoas Muscle	Psoas
22	chr6:36097800-36098600	Active TSS	Rectal Smooth Muscle	rectum
23	chr6:36097800-36098800	Active TSS	Fetal Intestine Small	intestine
24	chr6:36097800-36099200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr6:36097800-36099200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:36097800-36099200	Active TSS	Brain Angular Gyrus	brain
27	chr6:36097800-36099200	Active TSS	Brain Anterior Caudate	brain
28	chr6:36097800-36099200	Active TSS	Fetal Intestine Large	intestine
29	chr6:36097800-36099400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr6:36097800-36099400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:36097800-36099600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:36098000-36098600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:36098000-36098600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:36098000-36098600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:36098000-36098600	Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr6:36098000-36098600	Active TSS	Primary B cells from peripheral blood	blood
37	chr6:36098000-36098600	Active TSS	Primary T cells fromperipheralblood	blood
38	chr6:36098000-36098600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:36098000-36098600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:36098000-36098600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:36098000-36098600	Active TSS	Aorta	Aorta
42	chr6:36098000-36098600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr6:36098000-36098600	Weak transcription	Fetal Kidney	kidney
44	chr6:36098000-36098600	Active TSS	Fetal Thymus	thymus
45	chr6:36098000-36098600	Active TSS	Ovary	ovary
46	chr6:36098000-36098600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr6:36098000-36098600	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr6:36098000-36098600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
49	chr6:36098000-36098600	Enhancers	Stomach Mucosa	stomach
50	chr6:36098000-36098600	Active TSS	NHEK	skin

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