Variant report

Variant	rs17659749
Chromosome Location	chr18:12991521-12991522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:478)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:478 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr18:12990599-12992272	MCF-7	breast:	n/a	n/a
2	CTCF	chr18:12991486-12991563	Kidney_OC	kidney:	n/a	chr18:12991543-12991556
3	NRF1	chr18:12991142-12991719	H1-hESC	embryonic stem cell:	n/a	chr18:12991298-12991307 chr18:12991344-12991353 chr18:12991344-12991358 chr18:12991343-12991354 chr18:12991344-12991355
4	MXI1	chr18:12990166-12992232	K562	blood:	n/a	n/a
5	RELA	chr18:12990731-12992053	GM18526	blood:	n/a	n/a
6	MAZ	chr18:12990674-12992082	IMR90	lung:	n/a	n/a
7	CTCF	chr18:12991400-12991550	AoAF	blood vessel:	n/a	n/a
8	FOSL2	chr18:12990923-12991803	HepG2	liver:	n/a	n/a
9	FOXP2	chr18:12991078-12991616	SK-N-MC	brain:	n/a	n/a
10	SIN3AK20	chr18:12990794-12991954	SK-N-SH	brain:	n/a	n/a
11	RCOR1	chr18:12989893-12992146	K562	blood:	n/a	n/a
12	CTCF	chr18:12991467-12991566	K562	blood:	n/a	chr18:12991543-12991556
13	TAF1	chr18:12990998-12991737	H1-neurons	neurons:	n/a	n/a
14	CTCF	chr18:12991460-12991610	GM12874	blood:	n/a	chr18:12991543-12991556
15	POLR2A	chr18:12989157-12991987	K562	blood:	n/a	n/a
16	POLR2A	chr18:12990682-12991919	GM12878	blood:	n/a	n/a
17	REST	chr18:12991150-12991825	A549	lung:	n/a	chr18:12991456-12991469 chr18:12991443-12991456
18	CTCF	chr18:12991480-12991630	Caco-2	colon:	n/a	chr18:12991543-12991556
19	KAP1	chr18:12990513-12992263	HEK293	kidney:	n/a	n/a
20	POLR2A	chr18:12990565-12991948	K562	blood:	n/a	n/a
21	MYC	chr18:12991004-12991770	MCF-7	breast:	n/a	n/a
22	USF1	chr18:12990980-12991556	ECC-1	luminal epithelium:	n/a	chr18:12991326-12991342 chr18:12991320-12991336
23	CTCF	chr18:12991371-12991662	MCF-7	breast:	n/a	chr18:12991543-12991556
24	CTCF	chr18:12991520-12991670	HMEC	breast:	n/a	chr18:12991543-12991556
25	CTCF	chr18:12991484-12991635	GM13977	blood:	n/a	chr18:12991543-12991556
26	RELA	chr18:12990732-12992081	GM18951	blood:	n/a	n/a
27	CHD2	chr18:12991018-12991695	HepG2	liver:	n/a	n/a
28	CTCF	chr18:12991400-12991550	Caco-2	colon:	n/a	n/a
29	CTCF	chr18:12991480-12991630	GM12864	blood:	n/a	chr18:12991543-12991556
30	JUND	chr18:12990794-12992048	K562	blood:	n/a	n/a
31	IRF1	chr18:12990890-12991971	K562	blood:	n/a	n/a
32	MAX	chr18:12990028-12991918	K562	blood:	n/a	n/a
33	SIN3AK20	chr18:12990974-12991794	HepG2	liver:	n/a	n/a
34	CREB1	chr18:12990674-12991865	HepG2	liver:	n/a	n/a
35	MAX	chr18:12990613-12991913	MCF-7	breast:	n/a	n/a
36	CTCF	chr18:12991400-12991550	SK-N-SH_RA	brain:	n/a	n/a
37	POLR2A	chr18:12990738-12991921	HEK293	kidney:	n/a	n/a
38	BRCA1	chr18:12990794-12991570	Hela-S3	cervix:	n/a	n/a
39	MYC	chr18:12990123-12991940	K562	blood:	n/a	n/a
40	MYC	chr18:12991001-12991803	MCF-7	breast:	n/a	n/a
41	POLR2A	chr18:12990838-12991887	A549	lung:	n/a	n/a
42	POLR2A	chr18:12990630-12991858	HCT-116	colon:	n/a	n/a
43	MAX	chr18:12990655-12991780	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr18:12991359-12991612	GM10266	blood:	n/a	chr18:12991543-12991556
45	POLR2A	chr18:12989077-12992444	GM12878	blood:	n/a	n/a
46	MAX	chr18:12990890-12991772	MCF-7	breast:	n/a	n/a
47	BHLHE40	chr18:12991118-12991918	HepG2	liver:	n/a	chr18:12991326-12991342 chr18:12991320-12991336
48	TCF12	chr18:12990769-12991858	ECC-1	luminal epithelium:	n/a	n/a
49	E2F4	chr18:12990593-12991599	GM12878	blood:	n/a	chr18:12991208-12991220 chr18:12991298-12991307 chr18:12991345-12991354
50	CTCF	chr18:12991365-12991642	GM19239	blood:	n/a	chr18:12991543-12991556

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12701267..12703413-chr18:12991110..12994892,3	K562	blood:
2	chr18:12990458..12991873-chr9:91932802..91933783,3	Hela-S3	cervix:
3	chr18:12991038..12991997-chr6:99872882..99873671,2	Hela-S3	cervix:
4	chr18:12946883..12949783-chr18:12990489..12993346,5	MCF-7	breast:
5	chr12:57081960..57082470-chr18:12991251..12991751,2	NB4	blood:
6	chr17:17740122..17740700-chr18:12990991..12991588,2	Hela-S3	cervix:
7	chr18:12945719..12950670-chr18:12989123..12995651,19	K562	blood:
8	chr17:61523171..61523824-chr18:12990700..12991581,2	Hela-S3	cervix:
9	chr18:12971249..12974224-chr18:12989349..12991861,2	MCF-7	breast:
10	chr18:12701527..12703834-chr18:12990213..12992610,2	K562	blood:
11	chr18:12944429..12952802-chr18:12987284..12998193,21	K562	blood:
12	chr18:12945869..12950267-chr18:12985686..12992743,10	MCF-7	breast:
13	chr18:12990875..12991863-chr22:31884946..31885786,2	Hela-S3	cervix:
14	chr18:12375636..12378066-chr18:12991064..12992748,2	K562	blood:
15	chr18:12991401..12992947-chr18:13092444..13094824,2	K562	blood:
16	chr15:73925842..73926561-chr18:12991102..12991902,2	Hela-S3	cervix:
17	chr18:12977438..12979296-chr18:12990126..12991644,2	K562	blood:
18	chr18:12991026..12991868-chr4:119199244..119200267,3	Hela-S3	cervix:
19	chr1:26606197..26607867-chr18:12991163..12992861,2	MCF-7	breast:
20	chr1:17231189..17232122-chr18:12990618..12991592,3	Hela-S3	cervix:
21	chr18:12990770..12991770-chr19:17336480..17337257,2	Hela-S3	cervix:
22	chr18:12701070..12703137-chr18:12990557..12992522,2	MCF-7	breast:
23	chr18:12990712..12991709-chr3:9438699..9439422,2	NB4	blood:
24	chr18:12991467..12993717-chr18:13539738..13542100,2	MCF-7	breast:
25	chr18:12990627..12994399-chr18:13026748..13030425,3	K562	blood:
26	chr18:12977796..12979633-chr18:12990126..12992980,2	K562	blood:
27	chr15:65588005..65588576-chr18:12991133..12991998,2	Hela-S3	cervix:
28	chr18:12536634..12538194-chr18:12991456..12994159,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266969	TF binding region
ENSG00000132424	Chromatin interaction
ENSG00000168137	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000272426	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000187742	Chromatin interaction
ENSG00000072310	Chromatin interaction
ENSG00000156642	Chromatin interaction
ENSG00000099330	Chromatin interaction
ENSG00000008283	Chromatin interaction
ENSG00000269893	Chromatin interaction
ENSG00000142669	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000101624	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10163827	0.89[ASN][1000 genomes]
rs11080617	0.97[ASN][1000 genomes]
rs11080618	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11661322	0.83[EUR][1000 genomes]
rs11661908	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11662634	0.89[ASN][1000 genomes]
rs11664213	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11664469	0.97[ASN][1000 genomes]
rs12605267	0.97[ASN][1000 genomes]
rs12607398	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12607919	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12953783	0.87[ASN][1000 genomes]
rs12957380	0.89[ASN][1000 genomes]
rs12960349	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12961596	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12963426	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12970503	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12971069	0.82[AMR][1000 genomes]
rs13381779	0.89[ASN][1000 genomes]
rs1523064	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17603207	0.91[ASN][1000 genomes]
rs17659689	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17659896	0.95[ASN][1000 genomes]
rs2015763	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2282540	0.85[ASN][1000 genomes]
rs2282541	0.92[ASN][1000 genomes]
rs28551661	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28654613	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34166083	0.99[ASN][1000 genomes]
rs34302481	0.95[ASN][1000 genomes]
rs35368962	0.99[ASN][1000 genomes]
rs35563947	0.95[ASN][1000 genomes]
rs3809914	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3976787	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499304	0.85[EUR][1000 genomes]
rs56263236	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58871601	0.84[EUR][1000 genomes]
rs68004799	0.99[ASN][1000 genomes]
rs7228684	0.93[ASN][1000 genomes]
rs7229869	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7230391	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7230435	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7234163	0.85[EUR][1000 genomes]
rs7234938	0.89[ASN][1000 genomes]
rs7236710	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7237711	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7239486	0.92[ASN][1000 genomes]
rs8083401	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8086882	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8089724	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8090667	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8092888	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8093236	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8093576	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8096860	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8566	0.99[ASN][1000 genomes]
rs9950241	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	esv3395285	chr18:12988952-12991750	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17659749	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs17659749	CEP192	cis	lung	GTEx
rs17659749	CEP192	cis	Adipose Subcutaneous	GTEx
rs17659749	CEP192	cis	Thyroid	GTEx
rs17659749	CEP192	cis	Esophagus Mucosa	GTEx
rs17659749	CEP192	cis	Esophagus Muscularis	GTEx
rs17659749	CEP192	cis	Artery Tibial	GTEx
rs17659749	CEP192	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12989600-12992400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr18:12990200-12992200	Active TSS	Stomach Smooth Muscle	stomach
3	chr18:12990200-12992600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr18:12990400-12992200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:12990400-12992200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:12990400-12992400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr18:12990400-12992800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:12990400-12992800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:12990400-12992800	Active TSS	Colonic Mucosa	Colon
10	chr18:12990400-12993000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:12990400-12993200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr18:12990400-12993200	Active TSS	A549	lung
13	chr18:12990400-12993200	Active TSS	NHLF	lung
14	chr18:12990600-12992000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr18:12990600-12992000	Active TSS	Esophagus	oesophagus
16	chr18:12990600-12992000	Active TSS	Left Ventricle	heart
17	chr18:12990600-12992000	Active TSS	Pancreas	Pancrea
18	chr18:12990600-12992200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr18:12990600-12992200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr18:12990600-12992200	Active TSS	Fetal Brain Male	brain
21	chr18:12990600-12992200	Active TSS	Placenta Amnion	Placenta Amnion
22	chr18:12990600-12992200	Bivalent/Poised TSS	HepG2	liver
23	chr18:12990600-12992400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr18:12990600-12992400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr18:12990600-12992400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr18:12990600-12992400	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr18:12990600-12992400	Active TSS	Fetal Intestine Small	intestine
28	chr18:12990600-12992400	Active TSS	Fetal Kidney	kidney
29	chr18:12990600-12992400	Active TSS	Fetal Muscle Trunk	muscle
30	chr18:12990600-12992400	Active TSS	Ovary	ovary
31	chr18:12990600-12992400	Active TSS	Right Atrium	heart
32	chr18:12990600-12992400	Active TSS	HSMMtube	muscle
33	chr18:12990600-12992600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr18:12990600-12992600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:12990600-12992600	Active TSS	Fetal Intestine Large	intestine
36	chr18:12990600-12992600	Active TSS	Psoas Muscle	Psoas
37	chr18:12990600-12992600	Active TSS	Right Ventricle	heart
38	chr18:12990600-12992600	Active TSS	NHDF-Ad	bronchial
39	chr18:12990600-12992800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr18:12990600-12992800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr18:12990600-12992800	Active TSS	K562	blood
42	chr18:12990600-12993000	Active TSS	GM12878-XiMat	blood
43	chr18:12990600-12993200	Active TSS	H1 Cell Line	embryonic stem cell
44	chr18:12990600-12993200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr18:12990600-12993200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:12990600-12993400	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr18:12990800-12991800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
48	chr18:12990800-12991800	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr18:12990800-12992000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr18:12990800-12992000	Active TSS	Primary monocytes fromperipheralblood	blood

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