Variant report

Variant	rs466886
Chromosome Location	chr6:33240699-33240700
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:112)
CpG islands
(count:0)
Chromatin interactive
region (count:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:112 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33238834-33246727	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:33238760-33241532	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:33238829-33246424	HepG2	liver:	n/a	n/a
4	PML	chr6:33238698-33243154	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:33238876-33241752	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:33238771-33246916	GM12891	blood:	n/a	n/a
7	MXI1	chr6:33238746-33241055	IMR90	lung:	n/a	n/a
8	POLR2A	chr6:33238903-33241409	GM12891	blood:	n/a	n/a
9	POLR2A	chr6:33239090-33241526	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr6:33238864-33240991	HCT-116	colon:	n/a	n/a
11	POLR2A	chr6:33238743-33246473	GM12892	blood:	n/a	n/a
12	TBL1XR1	chr6:33238847-33241192	K562	blood:	n/a	n/a
13	TEAD4	chr6:33238694-33241455	K562	blood:	n/a	n/a
14	MXI1	chr6:33238699-33243818	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr6:33238799-33249598	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr6:33240629-33240869	ECC-1	luminal epithelium:	n/a	n/a
17	TBP	chr6:33238928-33240936	Hela-S3	cervix:	n/a	n/a
18	PML	chr6:33238711-33241787	K562	blood:	n/a	n/a
19	POLR2A	chr6:33240639-33240833	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:33238786-33246484	HL-60	blood:	n/a	n/a
21	KAP1	chr6:33238894-33241036	K562	blood:	n/a	n/a
22	POLR2A	chr6:33238743-33246025	K562	blood:	n/a	n/a
23	HEY1	chr6:33238730-33245426	K562	blood:	n/a	chr6:33244975-33244990
24	POLR2A	chr6:33238841-33246850	SK-N-SH	brain:	n/a	n/a
25	CEBPB	chr6:33240366-33241462	GM12878	blood:	n/a	chr6:33240666-33240678
26	POLR2A	chr6:33238919-33241460	K562	blood:	n/a	n/a
27	POLR2A	chr6:33238813-33246944	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:33239173-33241412	HepG2	liver:	n/a	n/a
29	POLR2A	chr6:33238661-33247019	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr6:33238693-33247581	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr6:33239093-33241037	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr6:33239106-33241447	U87	brain:	n/a	n/a
33	CCNT2	chr6:33240694-33241077	K562	blood:	n/a	n/a
34	POLR2A	chr6:33238895-33241487	K562	blood:	n/a	n/a
35	POLR2A	chr6:33238873-33246380	K562	blood:	n/a	n/a
36	MYC	chr6:33238876-33240926	K562	blood:	n/a	n/a
37	POLR2A	chr6:33240547-33241580	U87	brain:	n/a	n/a
38	POLR2A	chr6:33238907-33243453	MCF-7	breast:	n/a	n/a
39	POLR2A	chr6:33238910-33246525	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr6:33238801-33246451	GM12892	blood:	n/a	n/a
41	STAT5A	chr6:33238840-33241038	K562	blood:	n/a	chr6:33240627-33240638
42	POLR2A	chr6:33238892-33240946	Raji	blood:	n/a	n/a
43	MYC	chr6:33239146-33240849	K562	blood:	n/a	n/a
44	RUNX3	chr6:33238812-33240766	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:33238973-33241654	NB4	blood:	n/a	n/a
46	NFIC	chr6:33238947-33240943	GM12878	blood:	n/a	n/a
47	TBL1XR1	chr6:33238876-33241079	K562	blood:	n/a	n/a
48	POLR2A	chr6:33238744-33241576	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr6:33238672-33247507	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:33238762-33241539	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33215556..33218937-chr6:33237888..33241355,8	MCF-7	breast:
2	chr6:33214775..33224346-chr6:33236521..33248678,40	K562	blood:
3	chr6:33163540..33178083-chr6:33236797..33246926,29	MCF-7	breast:
4	chr6:33239039..33242495-chr6:33357243..33362134,5	MCF-7	breast:
5	chr6:32935365..32941512-chr6:33237253..33242856,9	MCF-7	breast:
6	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
7	chr6:33240007..33241601-chr6:33553728..33555294,2	K562	blood:
8	chr6:32942493..32944074-chr6:33239373..33240940,2	K562	blood:
9	chr6:33239756..33241300-chr6:42712858..42715263,2	MCF-7	breast:
10	chr6:33171159..33172807-chr6:33239561..33241466,2	MCF-7	breast:
11	chr6:33238090..33243099-chr6:33279379..33286881,12	MCF-7	breast:
12	chr6:33239271..33241277-chr6:33383669..33386403,3	MCF-7	breast:
13	chr6:33168190..33170625-chr6:33239125..33244589,6	MCF-7	breast:
14	chr6:32942574..32944407-chr6:33239254..33240873,2	K562	blood:
15	chr6:33165702..33182742-chr6:33234718..33250379,54	K562	blood:
16	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
17	chr6:33238428..33241280-chr6:33357854..33362793,6	MCF-7	breast:
18	chr6:33237157..33241221-chr6:33375922..33380109,6	MCF-7	breast:
19	chr6:33237639..33241732-chr6:33383253..33390116,11	K562	blood:
20	chr6:33215322..33223570-chr6:33237379..33242085,16	MCF-7	breast:
21	chr6:33237328..33248026-chr6:33370896..33379989,29	K562	blood:
22	chr6:33238401..33240913-chr6:33381042..33383923,3	MCF-7	breast:
23	chr6:33240213..33242985-chr6:33384063..33385890,2	MCF-7	breast:
24	chr6:33164650..33184503-chr6:33230350..33245922,64	K562	blood:
25	chr6:32934872..32941448-chr6:33236243..33241295,9	MCF-7	breast:
26	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
27	chr6:32935501..32940970-chr6:33237778..33241596,10	K562	blood:
28	chr6:32819661..32822280-chr6:33238410..33240981,2	MCF-7	breast:
29	chr21:46236119..46237973-chr6:33239831..33242378,2	K562	blood:
30	chr6:33173334..33178624-chr6:33237900..33241664,7	MCF-7	breast:
31	chr6:33237283..33241357-chr6:33358017..33360541,6	K562	blood:
32	chr6:33237802..33241730-chr6:33382199..33389112,10	K562	blood:
33	chr6:32920379..32922659-chr6:33240003..33242483,2	MCF-7	breast:
34	chr6:33159618..33162340-chr6:33240515..33243062,2	K562	blood:
35	chr6:32933888..32938246-chr6:33239158..33241596,4	K562	blood:
36	chr13:91999607..92001112-chr6:33239163..33241434,2	K562	blood:

No data

Variant related genes	Relation type
B3GALT4	TF binding region
VPS52	TF binding region
RPS18	TF binding region
ENSG00000168394	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000240065	Chromatin interaction
ENSG00000204248	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000124659	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000225463	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000204228	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1704999	0.80[AFR][1000 genomes]
rs3445	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs458434	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs460568	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs461338	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462618	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464921	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9277956	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9277958	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9277965	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462893	chr6:33142539-33256471	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv602830	chr6:33142539-33256471	Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	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
4	nsv462894	chr6:33174783-33254665	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
5	nsv602831	chr6:33174783-33254665	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
6	nsv5249	chr6:33231743-33249478	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	62 gene(s)	inside rSNPs	diseases
7	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
rs466886	STK38	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33238600-33241800	Active TSS	GM12878-XiMat	blood
2	chr6:33238800-33240800	Active TSS	Ovary	ovary
3	chr6:33238800-33241200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:33238800-33241200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:33238800-33241200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:33238800-33241200	Active TSS	Lung	lung
7	chr6:33238800-33241200	Active TSS	Pancreas	Pancrea
8	chr6:33238800-33241200	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr6:33238800-33241400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr6:33238800-33241400	Active TSS	Right Atrium	heart
11	chr6:33238800-33241800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:33238800-33244800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:33239000-33240800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:33239000-33241000	Active TSS	HSMMtube	muscle
15	chr6:33239000-33241200	Active TSS	Esophagus	oesophagus
16	chr6:33239200-33240800	Active TSS	Right Ventricle	heart
17	chr6:33239200-33241200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr6:33239800-33240800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:33240000-33240800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr6:33240000-33240800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr6:33240000-33240800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:33240000-33240800	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr6:33240000-33240800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr6:33240000-33241000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:33240000-33241000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:33240000-33241200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr6:33240000-33241200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:33240000-33241200	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr6:33240000-33241400	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr6:33240000-33244800	Transcr. at gene 5' and 3'	Dnd41	blood
31	chr6:33240000-33245600	Transcr. at gene 5' and 3'	NHEK	skin
32	chr6:33240200-33240800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:33240200-33240800	Flanking Active TSS	Liver	Liver
34	chr6:33240200-33240800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:33240200-33241000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr6:33240200-33241000	Flanking Active TSS	Thymus	Thymus
37	chr6:33240200-33241200	Flanking Active TSS	Fetal Brain Female	brain
38	chr6:33240200-33241200	Flanking Active TSS	Fetal Heart	heart
39	chr6:33240200-33241200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr6:33240200-33241400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:33240200-33241400	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr6:33240200-33241400	Flanking Active TSS	Fetal Brain Male	brain
43	chr6:33240200-33242800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
44	chr6:33240200-33243400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
45	chr6:33240200-33244800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
46	chr6:33240200-33244800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
47	chr6:33240200-33244800	Transcr. at gene 5' and 3'	A549	lung
48	chr6:33240200-33244800	Transcr. at gene 5' and 3'	K562	blood
49	chr6:33240200-33245800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:33240400-33240800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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