Variant report

Variant	rs9950799
Chromosome Location	chr18:11980090-11980091
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	PRDM1	chr18:11980042-11980362	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr18:11980046-11981745	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr18:11979815-11984651	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr18:11979871-11982537	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr18:11979875-11982298	K562	blood:	n/a	chr18:11980676-11980686 chr18:11981195-11981205 chr18:11981509-11981521 chr18:11981001-11981010
6	MAX	chr18:11980060-11982421	A549	lung:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748
7	E2F6	chr18:11980084-11981760	H1-hESC	embryonic stem cell:	n/a	chr18:11980676-11980686 chr18:11981195-11981205 chr18:11981509-11981521 chr18:11981001-11981010
8	POLR2A	chr18:11980052-11981172	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr18:11979874-11982211	Raji	blood:	n/a	n/a
10	HCFC1	chr18:11979756-11982606	Hela-S3	cervix:	n/a	n/a
11	EP300	chr18:11979965-11981297	K562	blood:	n/a	chr18:11980046-11980055 chr18:11981211-11981227 chr18:11981201-11981217 chr18:11980542-11980558
12	MYC	chr18:11980031-11981196	MCF10A-Er-Src	breast:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
13	CHD1	chr18:11980053-11980753	H1-hESC	embryonic stem cell:	n/a	n/a
14	RCOR1	chr18:11980060-11982342	K562	blood:	n/a	n/a
15	TBP	chr18:11979960-11981278	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr18:11980045-11981120	K562	blood:	n/a	n/a
17	MYC	chr18:11979987-11982396	K562	blood:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748
18	POLR2A	chr18:11979763-11982760	HepG2	liver:	n/a	n/a
19	MYC	chr18:11980057-11981549	MCF10A-Er-Src	breast:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
20	POLR2A	chr18:11979955-11981066	K562	blood:	n/a	n/a
21	IRF1	chr18:11979950-11981184	K562	blood:	n/a	chr18:11980932-11980946 chr18:11981000-11981014 chr18:11981113-11981127 chr18:11980962-11980976
22	POLR2A	chr18:11979824-11982628	Hela-S3	cervix:	n/a	n/a
23	STAT1	chr18:11979964-11981148	Hela-S3	cervix:	n/a	n/a
24	UBTF	chr18:11980040-11982463	K562	blood:	n/a	n/a
25	POLR2A	chr18:11979779-11982710	HL-60	blood:	n/a	n/a
26	POLR2A	chr18:11980046-11981052	K562	blood:	n/a	n/a
27	STAT3	chr18:11980016-11980525	MCF10A-Er-Src	breast:	n/a	chr18:11980334-11980345
28	MAX	chr18:11980075-11981096	H1-hESC	embryonic stem cell:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
29	MYC	chr18:11980005-11981908	K562	blood:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748
30	MAZ	chr18:11979958-11982563	IMR90	lung:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748
31	MYC	chr18:11979965-11981220	K562	blood:	n/a	chr18:11980736-11980743 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11980733-11980748
32	POLR2A	chr18:11979971-11981744	K562	blood:	n/a	n/a
33	CEBPB	chr18:11980045-11981387	Hela-S3	cervix:	n/a	n/a
34	HEY1	chr18:11980059-11981195	HepG2	liver:	n/a	chr18:11981055-11981070
35	STAT3	chr18:11980065-11980514	MCF10A-Er-Src	breast:	n/a	chr18:11980334-11980345
36	MAFK	chr18:11980090-11981237	Hela-S3	cervix:	n/a	n/a
37	RFX5	chr18:11980059-11981694	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr18:11979844-11984663	HepG2	liver:	n/a	n/a
39	MAX	chr18:11979930-11982309	HepG2	liver:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748
40	POLR2A	chr18:11979964-11982508	Hela-S3	cervix:	n/a	n/a
41	TAL1	chr18:11980006-11981301	K562	blood:	n/a	n/a
42	POLR2A	chr18:11979938-11982295	MCF10A-Er-Src	breast:	n/a	n/a
43	MAX	chr18:11980027-11982357	HepG2	liver:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748
44	POLR2A	chr18:11980013-11981039	K562	blood:	n/a	n/a
45	POLR2A	chr18:11980034-11981856	K562	blood:	n/a	n/a
46	POLR2A	chr18:11980070-11981753	HEK293	kidney:	n/a	n/a
47	RCOR1	chr18:11979913-11981678	Hela-S3	cervix:	n/a	n/a
48	MAX	chr18:11980084-11982571	NB4	blood:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748
49	MYC	chr18:11979933-11981914	A549	lung:	n/a	chr18:11980736-11980743 chr18:11981882-11981892 chr18:11980734-11980745 chr18:11980735-11980745 chr18:11980735-11980744 chr18:11981808-11981817 chr18:11980733-11980748

No.	Distal block	Cell Line	Cell type
1	chr11:65194558..65195488-chr18:11979959..11980471,2	Hela-S3	cervix:
2	chr18:11979615..11982143-chr18:12376173..12378788,2	K562	blood:
3	chr18:11848937..11853647-chr18:11979272..11982109,5	K562	blood:
4	chr18:11906925..11910950-chr18:11978930..11983753,7	MCF-7	breast:
5	chr18:11972047..11973789-chr18:11978802..11980433,2	MCF-7	breast:
6	chr18:11978568..11983192-chr18:11993805..11998306,5	MCF-7	breast:
7	chr18:11979089..11980849-chr18:12109709..12111299,2	K562	blood:
8	chr18:11908235..11908915-chr18:11980031..11980748,2	Hela-S3	cervix:
9	chr18:11906869..11908788-chr18:11979428..11982249,2	K562	blood:
10	chr18:11977841..11980802-chr18:11983345..11984923,2	MCF-7	breast:
11	chr18:11979171..11983679-chr18:11993501..11995734,4	MCF-7	breast:
12	chr18:11848574..11852252-chr18:11979272..11982648,7	K562	blood:
13	chr18:11907153..11910661-chr18:11980045..11982514,4	MCF-7	breast:

Variant related genes	Relation type
IMPA2	TF binding region
ENSG00000267165	Chromatin interaction
ENSG00000154889	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000273141	Chromatin interaction
ENSG00000255112	Chromatin interaction
ENSG00000266955	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11659317	1.00[ASN][1000 genomes]
rs17593321	0.90[ASN][1000 genomes]
rs1787983	1.00[ASN][1000 genomes]
rs1787986	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2586219	1.00[ASN][1000 genomes]
rs2848459	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2849407	1.00[ASN][1000 genomes]
rs3889500	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59082529	0.91[ASN][1000 genomes]
rs610541	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs611930	1.00[ASN][1000 genomes]
rs612854	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62099883	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62099884	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62099886	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62099887	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62099888	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62099891	0.86[EUR][1000 genomes]
rs62099892	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62099914	0.90[ASN][1000 genomes]
rs62099915	0.90[ASN][1000 genomes]
rs661450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs7244659	1.00[ASN][1000 genomes]
rs8087838	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091268	1.00[ASN][1000 genomes]
rs9960943	1.00[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	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription 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	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv576495	chr18:11917410-11986557	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv909385	chr18:11938102-11986557	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
8	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv909387	chr18:11953187-11986557	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11964400-11980400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:11976600-11980200	Enhancers	Placenta	Placenta
3	chr18:11977000-11980200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:11977400-11980200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr18:11978600-11980200	Enhancers	Fetal Lung	lung
6	chr18:11979000-11980200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr18:11979000-11980200	Enhancers	Fetal Stomach	stomach
8	chr18:11979000-11980400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr18:11979000-11980800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr18:11979200-11980200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr18:11979200-11980200	Enhancers	Stomach Mucosa	stomach
12	chr18:11979600-11980200	Enhancers	Fetal Muscle Trunk	muscle
13	chr18:11979800-11980200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr18:11979800-11980200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr18:11979800-11980200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr18:11979800-11980200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr18:11979800-11980200	Enhancers	Esophagus	oesophagus
18	chr18:11979800-11980200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr18:11979800-11980200	Enhancers	Fetal Intestine Large	intestine
20	chr18:11979800-11980200	Enhancers	Fetal Intestine Small	intestine
21	chr18:11979800-11980200	Enhancers	Fetal Muscle Leg	muscle
22	chr18:11979800-11980200	Enhancers	Lung	lung
23	chr18:11979800-11980200	Enhancers	Rectal Smooth Muscle	rectum
24	chr18:11979800-11980200	Flanking Active TSS	A549	lung
25	chr18:11979800-11980200	Enhancers	HMEC	breast
26	chr18:11979800-11980200	Enhancers	NHLF	lung
27	chr18:11979800-11980400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr18:11979800-11980400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:11979800-11980400	Enhancers	Primary B cells from peripheral blood	blood
30	chr18:11979800-11980400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr18:11979800-11980400	Enhancers	Pancreas	Pancrea
32	chr18:11979800-11980400	Flanking Active TSS	HepG2	liver
33	chr18:11979800-11980600	Flanking Active TSS	Liver	Liver
34	chr18:11979800-11980600	Enhancers	Fetal Heart	heart
35	chr18:11979800-11980600	Enhancers	Small Intestine	intestine
36	chr18:11979800-11980600	Flanking Active TSS	Hela-S3	cervix
37	chr18:11980000-11980200	Active TSS	H1 Cell Line	embryonic stem cell
38	chr18:11980000-11980200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr18:11980000-11980200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr18:11980000-11980200	Enhancers	Primary T cells from cord blood	blood
41	chr18:11980000-11980200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr18:11980000-11980200	Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr18:11980000-11980200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr18:11980000-11980200	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr18:11980000-11980200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:11980000-11980200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr18:11980000-11980200	Enhancers	Adipose Nuclei	Adipose
48	chr18:11980000-11980200	Enhancers	Brain Angular Gyrus	brain
49	chr18:11980000-11980200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr18:11980000-11980200	Enhancers	Colon Smooth Muscle	Colon

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