Variant report

Variant	rs1061801
Chromosome Location	chr6:33282338-33282339
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	RCOR1	chr6:33282234-33283117	K562	blood:	n/a	n/a
2	POLR2A	chr6:33281146-33283366	HUVEC	blood vessel:	n/a	n/a
3	EP300	chr6:33282215-33282635	HepG2	liver:	n/a	n/a
4	EP300	chr6:33281578-33282506	GM12878	blood:	n/a	chr6:33281860-33281874
5	TCF7L2	chr6:33282278-33282592	PANC-1	pancreas:	n/a	n/a
6	HDAC2	chr6:33282232-33282616	HepG2	liver:	n/a	n/a
7	PML	chr6:33280132-33282847	GM12878	blood:	n/a	n/a
8	RCOR1	chr6:33281570-33283179	K562	blood:	n/a	n/a
9	POLR2A	chr6:33281097-33283399	PANC-1	pancreas:	n/a	n/a
10	MXI1	chr6:33281486-33283181	K562	blood:	n/a	n/a
11	EGR1	chr6:33282066-33282597	GM12878	blood:	n/a	chr6:33282071-33282084 chr6:33282075-33282085 chr6:33282076-33282086
12	REST	chr6:33281220-33282338	HL-60	blood:	n/a	n/a
13	TEAD4	chr6:33280036-33283539	K562	blood:	n/a	n/a
14	EP300	chr6:33281698-33282649	GM12878	blood:	n/a	chr6:33281860-33281874
15	MYC	chr6:33282337-33282680	NB4	blood:	n/a	chr6:33282512-33282522
16	NR2F2	chr6:33281524-33282992	K562	blood:	n/a	chr6:33282459-33282474
17	RELA	chr6:33280470-33282720	GM18505	blood:	n/a	chr6:33281902-33281911 chr6:33281902-33281911
18	NFATC1	chr6:33282080-33282721	GM12878	blood:	n/a	n/a
19	RAD21	chr6:33280948-33282567	IMR90	lung:	n/a	n/a
20	POLR2A	chr6:33280818-33283534	GM12892	blood:	n/a	n/a
21	RELA	chr6:33280347-33282735	GM10847	blood:	n/a	chr6:33281902-33281911 chr6:33281902-33281911
22	YY1	chr6:33282194-33282661	GM12878	blood:	n/a	n/a
23	CHD1	chr6:33280438-33282580	GM12878	blood:	n/a	n/a
24	RUNX3	chr6:33280199-33282777	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:33280375-33283561	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr6:33282277-33282575	A549	lung:	n/a	n/a
27	POLR2A	chr6:33280354-33283211	GM12892	blood:	n/a	n/a
28	FOS	chr6:33282311-33282508	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr6:33282079-33282635	HepG2	liver:	n/a	n/a
30	SIN3A	chr6:33280946-33283091	GM12878	blood:	n/a	n/a
31	CCNT2	chr6:33282338-33283095	K562	blood:	n/a	n/a
32	POLR2A	chr6:33280288-33283297	MCF-7	breast:	n/a	n/a
33	BCL3	chr6:33281423-33282795	A549	lung:	n/a	chr6:33281860-33281869 chr6:33281866-33281875 chr6:33282075-33282084
34	STAT1	chr6:33281581-33282612	GM12878	blood:	n/a	chr6:33281864-33281875 chr6:33282071-33282083
35	RELA	chr6:33280373-33282911	GM19099	blood:	n/a	chr6:33281902-33281911 chr6:33281902-33281911
36	EGR1	chr6:33282235-33282396	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:33280764-33283332	GM12892	blood:	n/a	n/a
38	POLR2A	chr6:33280121-33283446	K562	blood:	n/a	n/a
39	POLR2A	chr6:33281077-33282629	Hela-S3	cervix:	n/a	n/a
40	USF2	chr6:33282234-33282825	Hela-S3	cervix:	n/a	chr6:33282452-33282463
41	FOXM1	chr6:33281111-33282570	GM12878	blood:	n/a	n/a
42	TCF12	chr6:33281215-33283124	A549	lung:	n/a	chr6:33282034-33282044
43	SP1	chr6:33282071-33282683	A549	lung:	n/a	chr6:33282074-33282086 chr6:33282075-33282085 chr6:33282076-33282085 chr6:33282596-33282607 chr6:33282074-33282086 chr6:33282075-33282084 chr6:33282075-33282089
44	POLR2A	chr6:33280417-33283656	PBDE	blood:	n/a	n/a
45	NR2F2	chr6:33282024-33282918	K562	blood:	n/a	chr6:33282459-33282474
46	EP300	chr6:33282134-33282754	A549	lung:	n/a	n/a
47	ELK1	chr6:33282212-33282651	K562	blood:	n/a	n/a
48	IRF1	chr6:33280345-33283267	K562	blood:	n/a	chr6:33281864-33281876 chr6:33281857-33281877 chr6:33281864-33281877 chr6:33281417-33281427 chr6:33281863-33281877 chr6:33281864-33281875 chr6:33280706-33280720 chr6:33281853-33281870 chr6:33281858-33281869 chr6:33281864-33281877 chr6:33281865-33281879 chr6:33281859-33281876 chr6:33281859-33281869 chr6:33281853-33281874 chr6:33281864-33281878 chr6:33281861-33281878 chr6:33281861-33281875 chr6:33282072-33282086 chr6:33281864-33281877 chr6:33281859-33281873 chr6:33281863-33281874 chr6:33281855-33281869 chr6:33281865-33281875
49	FOS	chr6:33282330-33282530	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr6:33280902-33283139	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33282313-33282363	LNCaP	prostate:	n/a
2	chr6:33282321-33282371	ovcar-3	ovarian:	n/a
3	chr6:33282330-33282380	A549	lung:	n/a
4	chr6:33282313-33282363	Hela-S3	cervix:	n/a
5	chr6:33282313-33282363	HNPCEpiC	eye:	n/a
6	chr6:33282321-33282371	AG04449	skin:	fetal
7	chr6:33282330-33282380	BJ	skin:	n/a
8	chr6:33282313-33282363	SK-N-MC	brain:	n/a
9	chr6:33282321-33282371	AoSMC	blood vessel:	n/a
10	chr6:33282321-33282371	GM06990	blood:	n/a
11	chr6:33282313-33282363	A549	lung:	n/a
12	chr6:33282321-33282371	AG04450	lung:	fetal
13	chr6:33282330-33282380	GM19239	blood:	n/a
14	chr6:33282313-33282363	MCF-7	breast:	n/a
15	chr6:33282321-33282371	HRPEpiC	eye:	n/a
16	chr6:33282321-33282371	ECC-1	luminal epithelium:	n/a
17	chr6:33282321-33282371	SK-N-MC	brain:	n/a
18	chr6:33282330-33282380	CMK	blood:	n/a
19	chr6:33282330-33282380	IMR90	lung:	fetal
20	chr6:33282330-33282380	HCM	heart:	n/a
21	chr6:33282321-33282371	SK-N-SH	brain:	n/a
22	chr6:33282313-33282363	GM12878	blood:	n/a
23	chr6:33282321-33282371	CMK	blood:	n/a
24	chr6:33282321-33282371	U87	brain:	n/a
25	chr6:33282330-33282380	NH-A	brain:	n/a
26	chr6:33282321-33282371	HEK293	kidney:	embryo
27	chr6:33282321-33282371	RPTEC	kidney:	n/a
28	chr6:33282313-33282363	HEEpiC	esophagus:	n/a
29	chr6:33282313-33282363	Hepatocyte	liver:	n/a
30	chr6:33282313-33282363	HRE	kidney:	n/a
31	chr6:33282313-33282363	NB4	blood:	n/a
32	chr6:33282321-33282371	LNCaP	prostate:	n/a
33	chr6:33282321-33282371	HRCEpiC	kidney:	n/a
34	chr6:33282330-33282380	SK-N-MC	brain:	n/a
35	chr6:33282330-33282380	HRCEpiC	kidney:	n/a
36	chr6:33282313-33282363	PFSK-1	brain:	n/a
37	chr6:33282330-33282380	HMEC	breast:	n/a
38	chr6:33282330-33282380	HEEpiC	esophagus:	n/a
39	chr6:33282330-33282380	SK-N-SH	brain:	n/a
40	chr6:33282330-33282380	GM12891	blood:	n/a
41	chr6:33282313-33282363	NT2-D1	testis:	n/a
42	chr6:33282330-33282380	Hepatocyte	liver:	n/a
43	chr6:33282321-33282371	SAEC	small airway:	n/a
44	chr6:33282330-33282380	Hela-S3	cervix:	n/a
45	chr6:33282321-33282371	AG09319	gingival:	n/a
46	chr6:33282321-33282371	HCPEpiC	choroid plexus:	n/a
47	chr6:33282313-33282363	GM06990	blood:	n/a
48	chr6:33282321-33282371	T-47D	breast:	n/a
49	chr6:33282313-33282363	AG09309	skin:	n/a
50	chr6:33282313-33282363	NH-A	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33167013..33169892-chr6:33280381..33282720,3	MCF-7	breast:
2	chr6:33238090..33243099-chr6:33279379..33286881,12	MCF-7	breast:
3	chr6:33280452..33282497-chr6:33377188..33378997,2	MCF-7	breast:
4	chr6:33280766..33282554-chr6:33333161..33335162,2	K562	blood:
5	chr6:33280908..33284579-chr6:33359142..33361187,5	K562	blood:
6	chr6:33259755..33275794-chr6:33276314..33291745,68	MCF-7	breast:
7	chr6:33215997..33218425-chr6:33280174..33283199,3	K562	blood:
8	chr6:32936236..32938607-chr6:33279588..33282413,3	MCF-7	breast:
9	chr11:33757523..33758138-chr6:33281662..33282491,2	Hela-S3	cervix:
10	chr6:33279220..33282454-chr6:33357653..33360404,5	MCF-7	breast:
11	chr19:14529814..14530438-chr6:33281601..33282533,2	Hela-S3	cervix:
12	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
13	chr16:56965612..56966446-chr6:33281998..33282624,2	Hela-S3	cervix:
14	chr6:33256218..33259091-chr6:33279064..33284854,6	MCF-7	breast:
15	chr17:7382482..7385239-chr6:33280198..33282715,2	MCF-7	breast:
16	chr6:33279097..33283546-chr6:33386045..33390564,5	MCF-7	breast:
17	chr6:33243260..33246626-chr6:33279357..33283682,8	MCF-7	breast:
18	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
19	chr6:33281855..33283498-chr6:33357981..33360061,3	MCF-7	breast:
20	chr17:29233009..29233845-chr6:33281938..33282496,2	Hela-S3	cervix:
21	chr6:33280708..33283139-chr6:33358214..33362149,5	K562	blood:

Variant related genes	Relation type
TAPBP	TF binding region
TAPBP	CpG island
ENSG00000085063	Chromatin interaction
ENSG00000172171	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000123136	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000184060	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000259224	Chromatin interaction
ENSG00000228285	Chromatin interaction
ENSG00000051108	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1800837	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3445	0.81[ASN][1000 genomes]
rs458434	0.81[ASN][1000 genomes]
rs9277988	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1061801	STK38	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33279600-33282400	Active TSS	NHDF-Ad	bronchial
2	chr6:33279800-33282400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:33279800-33282600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:33279800-33282600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33279800-33282800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:33279800-33283000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:33279800-33283200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:33280000-33282600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:33280000-33283000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:33280000-33283200	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr6:33280200-33282400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:33280200-33282400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr6:33280200-33282400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:33280200-33282400	Active TSS	Fetal Kidney	kidney
15	chr6:33280200-33282400	Active TSS	Lung	lung
16	chr6:33280200-33282400	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr6:33280200-33282400	Active TSS	Stomach Mucosa	stomach
18	chr6:33280200-33282400	Active TSS	GM12878-XiMat	blood
19	chr6:33280200-33282400	Active TSS	NHLF	lung
20	chr6:33280200-33282600	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:33280200-33282600	Active TSS	Ovary	ovary
22	chr6:33280200-33283200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr6:33280400-33282400	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr6:33280400-33282400	Active TSS	Colon Smooth Muscle	Colon
25	chr6:33280400-33282400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:33280400-33282400	Flanking Active TSS	Fetal Brain Male	brain
27	chr6:33280400-33282400	Active TSS	Fetal Intestine Large	intestine
28	chr6:33280400-33282400	Active TSS	Spleen	Spleen
29	chr6:33280400-33282400	Bivalent/Poised TSS	HepG2	liver
30	chr6:33280400-33282400	Active TSS	HMEC	breast
31	chr6:33280400-33282400	Active TSS	NHEK	skin
32	chr6:33280400-33282600	Active TSS	H1 Cell Line	embryonic stem cell
33	chr6:33280400-33282600	Active TSS	Aorta	Aorta
34	chr6:33280400-33283000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr6:33280600-33282400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:33280600-33282400	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr6:33280600-33282400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:33280600-33282400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:33280600-33282400	Active TSS	Brain Angular Gyrus	brain
40	chr6:33280600-33282400	Active TSS	Brain Anterior Caudate	brain
41	chr6:33280600-33282400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:33280600-33282400	Active TSS	Colonic Mucosa	Colon
43	chr6:33280600-33282400	Active TSS	Esophagus	oesophagus
44	chr6:33280600-33282400	Active TSS	Gastric	stomach
45	chr6:33280600-33282400	Active TSS	Pancreas	Pancrea
46	chr6:33280600-33282400	Active TSS	Psoas Muscle	Psoas
47	chr6:33280600-33282400	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr6:33280600-33282400	Active TSS	Rectal Smooth Muscle	rectum
49	chr6:33280600-33282400	Active TSS	HSMMtube	muscle
50	chr6:33280600-33282400	Active TSS	Monocytes-CD14+_RO01746	blood

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