Variant report

Variant	rs461338
Chromosome Location	chr6:33218180-33218181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33215890-33218603	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:33216129-33218664	K562	blood:	n/a	n/a
3	POLR2A	chr6:33218111-33218899	K562	blood:	n/a	n/a
4	POLR2A	chr6:33216349-33218931	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:33216690-33218371	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr6:33216658-33218231	K562	blood:	n/a	n/a
7	POLR2A	chr6:33216135-33218327	K562	blood:	n/a	n/a
8	POLR2A	chr6:33216575-33218371	SK-N-SH	brain:	n/a	n/a
9	NR2F2	chr6:33216074-33218495	K562	blood:	n/a	n/a
10	FOS	chr6:33218022-33218424	MCF10A-Er-Src	breast:	n/a	chr6:33218190-33218201
11	FOS	chr6:33218001-33218417	MCF10A-Er-Src	breast:	n/a	chr6:33218190-33218201
12	POLR2A	chr6:33216055-33218631	PANC-1	pancreas:	n/a	n/a
13	MXI1	chr6:33215923-33218584	IMR90	lung:	n/a	n/a
14	SMARCC1	chr6:33216974-33218600	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:33216103-33218534	IMR90	lung:	n/a	n/a
16	MAZ	chr6:33215638-33218697	IMR90	lung:	n/a	chr6:33215641-33215651 chr6:33217058-33217068
17	POLR2A	chr6:33218018-33218370	U87	brain:	n/a	n/a
18	POLR2A	chr6:33216087-33218389	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr6:33216586-33218380	GM12892	blood:	n/a	n/a
20	MYC	chr6:33218098-33218392	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr6:33216148-33218579	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:33216097-33218552	K562	blood:	n/a	n/a
23	POLR2A	chr6:33218062-33218387	U87	brain:	n/a	n/a
24	STAT3	chr6:33218096-33218380	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr6:33216613-33218246	GM12891	blood:	n/a	n/a
26	STAT3	chr6:33218095-33218385	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr6:33217833-33218579	Hela-S3	cervix:	n/a	n/a
28	FOS	chr6:33218014-33218396	MCF10A-Er-Src	breast:	n/a	chr6:33218190-33218201
29	FOS	chr6:33217890-33218377	HUVEC	blood vessel:	n/a	chr6:33218190-33218201
30	MYC	chr6:33218163-33218350	MCF10A-Er-Src	breast:	n/a	n/a
31	JUN	chr6:33215803-33218637	K562	blood:	n/a	chr6:33217287-33217296 chr6:33217081-33217090
32	FOS	chr6:33218026-33218380	MCF10A-Er-Src	breast:	n/a	chr6:33218190-33218201
33	POLR2A	chr6:33218062-33218345	U87	brain:	n/a	n/a
34	STAT3	chr6:33218061-33218348	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr6:33216768-33218182	GM12892	blood:	n/a	n/a
36	POLR2A	chr6:33216639-33218526	GM12892	blood:	n/a	n/a
37	POLR2A	chr6:33216169-33219719	HepG2	liver:	n/a	n/a
38	STAT3	chr6:33218064-33218374	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33172848..33181857-chr6:33213902..33220839,20	K562	blood:
2	chr6:33214841..33218494-chr6:33265669..33268981,6	K562	blood:
3	chr6:32942617..32945214-chr6:33216958..33219168,2	MCF-7	breast:
4	chr6:33166770..33170523-chr6:33215373..33219717,12	K562	blood:
5	chr6:33165570..33177648-chr6:33213944..33219124,23	MCF-7	breast:
6	chr6:33216736..33218315-chr6:33231569..33233281,2	MCF-7	breast:
7	chr6:33215556..33218937-chr6:33237888..33241355,8	MCF-7	breast:
8	chr6:33204555..33207456-chr6:33217202..33219174,2	MCF-7	breast:
9	chr6:33170516..33184004-chr6:33208467..33219908,34	K562	blood:
10	chr6:33164335..33170248-chr6:33215022..33224434,19	K562	blood:
11	chr6:33170716..33172526-chr6:33215536..33218522,2	K562	blood:
12	chr6:33176077..33178055-chr6:33215856..33218237,2	MCF-7	breast:
13	chr6:32934886..32941336-chr6:33214658..33220920,14	K562	blood:
14	chr6:32936711..32941313-chr6:33214829..33219433,9	K562	blood:
15	chr6:33215322..33223570-chr6:33237379..33242085,16	MCF-7	breast:
16	chr6:33166870..33169148-chr6:33216784..33219344,3	MCF-7	breast:
17	chr6:33217011..33220390-chr6:33230294..33232709,3	K562	blood:
18	chr6:33215839..33219931-chr6:33265339..33267743,5	MCF-7	breast:
19	chr6:33217871..33219670-chr6:33233287..33236131,2	K562	blood:
20	chr6:33214775..33224346-chr6:33236521..33248678,40	K562	blood:
21	chr6:33215997..33218425-chr6:33280174..33283199,3	K562	blood:
22	chr6:32940485..32942579-chr6:33215406..33218634,4	MCF-7	breast:
23	chr6:33215927..33218801-chr6:33244102..33245865,2	MCF-7	breast:
24	chr6:33164335..33166763-chr6:33216508..33219073,2	K562	blood:
25	chr6:32935631..32940142-chr6:33214930..33218579,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS18-2	chr6:33218056-33218488	ENSG00000232940.1

No data

Variant related genes	Relation type
ENSG00000272217	TF binding region
ENSG00000204227	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000225463	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000223457	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3445	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs458434	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs460568	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs462618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464921	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466886	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9277956	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9277958	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9277965	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33215600-33218200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:33216200-33218200	Flanking Active TSS	NH-A	brain
3	chr6:33216600-33218600	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr6:33217000-33218200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:33217400-33218200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr6:33217400-33218200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:33217400-33218200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:33217400-33218200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:33217400-33218200	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr6:33217400-33218200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr6:33217400-33218200	Flanking Active TSS	Dnd41	blood
12	chr6:33217400-33218200	Flanking Active TSS	NHLF	lung
13	chr6:33217400-33218200	Flanking Active TSS	Osteobl	bone
14	chr6:33217400-33218400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:33217400-33218400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr6:33217400-33218400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:33217400-33218400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:33217400-33218600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:33217400-33218600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:33217400-33218600	Flanking Active TSS	NHDF-Ad	bronchial
21	chr6:33217400-33234200	Weak transcription	Small Intestine	intestine
22	chr6:33217600-33218200	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr6:33217600-33218200	Flanking Active TSS	GM12878-XiMat	blood
24	chr6:33217600-33218400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:33217600-33218400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:33217600-33218800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:33217600-33218800	Flanking Active TSS	Hela-S3	cervix
28	chr6:33217600-33219000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:33217800-33218200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:33217800-33218200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:33217800-33218200	Enhancers	Fetal Brain Male	brain
32	chr6:33217800-33218200	Flanking Active TSS	HepG2	liver
33	chr6:33217800-33218400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:33217800-33218400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:33217800-33218400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
36	chr6:33217800-33218400	Enhancers	Fetal Heart	heart
37	chr6:33217800-33218400	Enhancers	Pancreas	Pancrea
38	chr6:33217800-33218600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr6:33217800-33218600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr6:33217800-33231200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:33217800-33231200	Weak transcription	Aorta	Aorta
42	chr6:33217800-33231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:33218000-33218200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:33218000-33218200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:33218000-33218200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:33218000-33218200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr6:33218000-33218200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:33218000-33218200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:33218000-33218200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:33218000-33218200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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