Variant report

Variant	rs17221597
Chromosome Location	chr6:33238892-33238893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:138)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:138 , 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	GABPA	chr6:33238784-33240356	A549	lung:	n/a	n/a
8	MXI1	chr6:33238746-33241055	IMR90	lung:	n/a	n/a
9	TCF12	chr6:33238761-33240321	A549	lung:	n/a	n/a
10	YY1	chr6:33238890-33240287	K562	blood:	n/a	chr6:33239424-33239444
11	POLR2A	chr6:33238864-33240991	HCT-116	colon:	n/a	n/a
12	RELA	chr6:33238876-33240243	GM19193	blood:	n/a	n/a
13	POLR2A	chr6:33238743-33246473	GM12892	blood:	n/a	n/a
14	TBL1XR1	chr6:33238847-33241192	K562	blood:	n/a	n/a
15	TEAD4	chr6:33238694-33241455	K562	blood:	n/a	n/a
16	MYC	chr6:33238842-33240651	K562	blood:	n/a	n/a
17	MXI1	chr6:33238699-33243818	SK-N-SH	brain:	n/a	n/a
18	YY1	chr6:33238752-33240248	GM12878	blood:	n/a	chr6:33239424-33239444 chr6:33238840-33238848 chr6:33238835-33238854
19	POLR2A	chr6:33238799-33249598	PANC-1	pancreas:	n/a	n/a
20	CEBPB	chr6:33238824-33240114	K562	blood:	n/a	n/a
21	PML	chr6:33238711-33241787	K562	blood:	n/a	n/a
22	EP300	chr6:33238872-33240375	GM12878	blood:	n/a	n/a
23	MAX	chr6:33238848-33240347	NB4	blood:	n/a	n/a
24	POLR2A	chr6:33238786-33246484	HL-60	blood:	n/a	n/a
25	POLR2A	chr6:33238743-33246025	K562	blood:	n/a	n/a
26	SIX5	chr6:33238774-33240259	A549	lung:	n/a	n/a
27	HEY1	chr6:33238730-33245426	K562	blood:	n/a	chr6:33244975-33244990
28	REST	chr6:33238669-33240570	H1-neurons	neurons:	n/a	n/a
29	GABPA	chr6:33238742-33240303	SK-N-SH	brain:	n/a	n/a
30	NFIC	chr6:33238877-33240336	HepG2	liver:	n/a	n/a
31	PML	chr6:33238747-33240578	K562	blood:	n/a	n/a
32	POLR2A	chr6:33238841-33246850	SK-N-SH	brain:	n/a	n/a
33	ATF2	chr6:33238810-33240271	GM12878	blood:	n/a	n/a
34	YY1	chr6:33238618-33240190	H1-hESC	embryonic stem cell:	n/a	chr6:33239424-33239444 chr6:33238840-33238848 chr6:33238835-33238854
35	CREB1	chr6:33238681-33240414	HepG2	liver:	n/a	n/a
36	YY1	chr6:33238743-33240148	GM12878	blood:	n/a	chr6:33239424-33239444 chr6:33238840-33238848 chr6:33238835-33238854
37	POLR2A	chr6:33238813-33246944	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:33238661-33247019	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr6:33238693-33247581	SK-N-MC	brain:	n/a	n/a
40	TRIM28	chr6:33238750-33240558	K562	blood:	n/a	n/a
41	TAF1	chr6:33238790-33240541	ECC-1	luminal epithelium:	n/a	n/a
42	CBX3	chr6:33238687-33240308	K562	blood:	n/a	n/a
43	MTA3	chr6:33238814-33240595	GM12878	blood:	n/a	n/a
44	RUNX3	chr6:33238850-33240276	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:33238873-33246380	K562	blood:	n/a	n/a
46	MYC	chr6:33238876-33240926	K562	blood:	n/a	n/a
47	ELK1	chr6:33238879-33240625	K562	blood:	n/a	n/a
48	CHD2	chr6:33238877-33240269	K562	blood:	n/a	n/a
49	POLR2A	chr6:33238801-33246451	GM12892	blood:	n/a	n/a
50	ZNF143	chr6:33238871-33240039	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:25 , 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	chr6:32935365..32941512-chr6:33237253..33242856,9	MCF-7	breast:
5	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
6	chr6:33238090..33243099-chr6:33279379..33286881,12	MCF-7	breast:
7	chr6:33165702..33182742-chr6:33234718..33250379,54	K562	blood:
8	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
9	chr6:33238428..33241280-chr6:33357854..33362793,6	MCF-7	breast:
10	chr6:33237157..33241221-chr6:33375922..33380109,6	MCF-7	breast:
11	chr6:33237639..33241732-chr6:33383253..33390116,11	K562	blood:
12	chr6:33215322..33223570-chr6:33237379..33242085,16	MCF-7	breast:
13	chr6:33237328..33248026-chr6:33370896..33379989,29	K562	blood:
14	chr6:33238401..33240913-chr6:33381042..33383923,3	MCF-7	breast:
15	chr6:33164650..33184503-chr6:33230350..33245922,64	K562	blood:
16	chr6:33238587..33240368-chr6:33290664..33293261,2	MCF-7	breast:
17	chr6:33238561..33240428-chr6:33421904..33423704,2	K562	blood:
18	chr6:32934872..32941448-chr6:33236243..33241295,9	MCF-7	breast:
19	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
20	chr6:32938812..32940970-chr6:33237778..33239459,3	K562	blood:
21	chr6:32935501..32940970-chr6:33237778..33241596,10	K562	blood:
22	chr6:32819661..32822280-chr6:33238410..33240981,2	MCF-7	breast:
23	chr6:33173334..33178624-chr6:33237900..33241664,7	MCF-7	breast:
24	chr6:33237283..33241357-chr6:33358017..33360541,6	K562	blood:
25	chr6:33237802..33241730-chr6:33382199..33389112,10	K562	blood:

No data

Variant related genes	Relation type
VPS52	TF binding region
RPS18	TF binding region
ENSG00000236104	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000225463	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000168394	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000240065	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17215196	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41266713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41266737	0.90[AFR][1000 genomes]
rs463302	0.82[AFR][1000 genomes]
rs6902176	0.86[AFR][1000 genomes]
rs72654476	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72654477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33237000-33239000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:33238000-33239000	Weak transcription	Spleen	Spleen
3	chr6:33238200-33239000	Flanking Active TSS	Dnd41	blood
4	chr6:33238200-33240600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:33238400-33240000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:33238400-33240200	Active TSS	K562	blood
7	chr6:33238400-33240400	Active TSS	Hela-S3	cervix
8	chr6:33238600-33239000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:33238600-33239000	Flanking Active TSS	HMEC	breast
10	chr6:33238600-33239000	Flanking Active TSS	NHEK	skin
11	chr6:33238600-33239200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr6:33238600-33239200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:33238600-33239400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:33238600-33239600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr6:33238600-33240000	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr6:33238600-33240200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:33238600-33240200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:33238600-33240400	Active TSS	HSMM	muscle
19	chr6:33238600-33241800	Active TSS	GM12878-XiMat	blood
20	chr6:33238800-33239000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:33238800-33239000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:33238800-33239000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr6:33238800-33239000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:33238800-33239000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:33238800-33239000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:33238800-33239000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:33238800-33239000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:33238800-33239000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:33238800-33239000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:33238800-33239000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr6:33238800-33239000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:33238800-33239000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:33238800-33239000	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr6:33238800-33239000	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr6:33238800-33239000	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr6:33238800-33239000	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr6:33238800-33239000	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr6:33238800-33239000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:33238800-33239000	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr6:33238800-33239000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr6:33238800-33239000	Flanking Active TSS	Esophagus	oesophagus
42	chr6:33238800-33239000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr6:33238800-33239000	Flanking Active TSS	Fetal Brain Female	brain
44	chr6:33238800-33239000	Flanking Active TSS	Fetal Heart	heart
45	chr6:33238800-33239000	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr6:33238800-33239000	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr6:33238800-33239000	Flanking Active TSS	Fetal Kidney	kidney
48	chr6:33238800-33239000	Flanking Active TSS	Fetal Lung	lung
49	chr6:33238800-33239000	Flanking Active TSS	Placenta	Placenta
50	chr6:33238800-33239000	Flanking Active TSS	Gastric	stomach

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