Variant report

Variant	rs72873549
Chromosome Location	chr18:11995703-11995704
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	SPI1	chr18:11995537-11995703	GM12878	blood:	n/a	n/a
2	CTCF	chr18:11995580-11995730	GM12878	blood:	n/a	chr18:11995586-11995602
3	RUNX3	chr18:11995381-11995753	GM12878	blood:	n/a	n/a
4	ELF1	chr18:11995386-11995775	K562	blood:	n/a	chr18:11995653-11995665
5	RFX5	chr18:11995534-11995706	GM12878	blood:	n/a	n/a
6	CTCF	chr18:11995478-11995743	Fibrobl	skin:	n/a	chr18:11995586-11995602
7	MAX	chr18:11994341-11995703	Hela-S3	cervix:	n/a	chr18:11994937-11994946 chr18:11994809-11994819
8	CUX1	chr18:11995425-11995753	K562	blood:	n/a	n/a
9	CTCF	chr18:11995456-11995740	HUVEC	blood vessel:	n/a	chr18:11995586-11995602
10	CTCF	chr18:11995496-11995712	GM13976	blood:	n/a	chr18:11995586-11995602
11	YY1	chr18:11995522-11995722	GM12891	blood:	n/a	n/a
12	RAD21	chr18:11995169-11995844	ECC-1	luminal epithelium:	n/a	chr18:11995700-11995714
13	RAD21	chr18:11995301-11995744	H1-hESC	embryonic stem cell:	n/a	chr18:11995700-11995714
14	MAZ	chr18:11994217-11996003	IMR90	lung:	n/a	chr18:11994937-11994946
15	CTCF	chr18:11995476-11995723	HepG2	liver:	n/a	chr18:11995586-11995602
16	CTCF	chr18:11995427-11995782	Spleen_OC	spleen:	n/a	chr18:11995586-11995602
17	PAX5	chr18:11995443-11995745	GM12878	blood:	n/a	n/a
18	MAX	chr18:11995318-11995784	NB4	blood:	n/a	n/a
19	SPI1	chr18:11995438-11995782	GM12891	blood:	n/a	n/a
20	MAX	chr18:11994311-11995863	HepG2	liver:	n/a	chr18:11994937-11994946 chr18:11994809-11994819
21	SMC3	chr18:11994455-11995935	HepG2	liver:	n/a	n/a
22	YY1	chr18:11995465-11995792	GM12878	blood:	n/a	n/a
23	BHLHE40	chr18:11995507-11995749	GM12878	blood:	n/a	n/a
24	CTCF	chr18:11995445-11995715	ECC-1	luminal epithelium:	n/a	chr18:11995586-11995602
25	ELF1	chr18:11995498-11995810	GM12878	blood:	n/a	chr18:11995653-11995665
26	SIN3A	chr18:11994863-11995742	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr18:11995331-11995733	A549	lung:	n/a	chr18:11995586-11995602
28	MAX	chr18:11994248-11995839	A549	lung:	n/a	chr18:11994937-11994946 chr18:11994809-11994819
29	POLR2A	chr18:11994227-11996555	HL-60	blood:	n/a	n/a
30	SMC3	chr18:11995340-11995765	GM12878	blood:	n/a	n/a
31	CTCF	chr18:11995426-11995729	HepG2	liver:	n/a	chr18:11995586-11995602
32	CTCF	chr18:11995349-11995879	K562	blood:	n/a	chr18:11995586-11995602
33	RCOR1	chr18:11995355-11995772	K562	blood:	n/a	n/a
34	TBL1XR1	chr18:11995504-11995728	GM12878	blood:	n/a	n/a
35	RAD21	chr18:11995196-11995812	HepG2	liver:	n/a	chr18:11995700-11995714
36	CTCF	chr18:11995478-11995722	Pancreas_OC	pancreas:	n/a	chr18:11995586-11995602
37	ELF1	chr18:11995457-11995750	K562	blood:	n/a	chr18:11995653-11995665
38	CTCF	chr18:11995560-11995710	NHEK	skin:	n/a	chr18:11995586-11995602
39	POLR2A	chr18:11993291-11997275	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr18:11995486-11995719	GM10248	blood:	n/a	chr18:11995586-11995602
41	CEBPB	chr18:11995363-11995735	Hela-S3	cervix:	n/a	n/a
42	CCNT2	chr18:11995458-11995739	K562	blood:	n/a	n/a
43	POLR2A	chr18:11994264-11995704	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr18:11995463-11995745	MCF-7	breast:	n/a	chr18:11995586-11995602
45	CTCF	chr18:11995461-11995763	GM12891	blood:	n/a	chr18:11995586-11995602
46	CTCF	chr18:11995457-11995747	Gliobla	brain:	n/a	chr18:11995586-11995602
47	POLR2A	chr18:11994498-11996051	K562	blood:	n/a	n/a
48	RAD21	chr18:11995372-11995709	SK-N-SH_RA	brain:	n/a	n/a
49	CTCF	chr18:11995366-11995800	H1-hESC	embryonic stem cell:	n/a	chr18:11995586-11995602
50	CTCF	chr18:11995473-11995749	A549	lung:	n/a	chr18:11995586-11995602

No.	Distal block	Cell Line	Cell type
1	chr18:11994002..11996965-chr18:12008009..12011015,3	MCF-7	breast:
2	chr18:11979171..11983679-chr18:11993501..11995734,4	MCF-7	breast:
3	chr18:11913714..11914470-chr18:11995363..11996159,2	MCF-7	breast:
4	chr18:11937478..11938603-chr18:11995051..11996237,21	K562	blood:
5	chr18:11654974..11655700-chr18:11995123..11996004,2	K562	blood:
6	chr18:11978568..11983192-chr18:11993805..11998306,5	MCF-7	breast:
7	chr18:11937069..11938706-chr18:11995081..11996087,16	MCF-7	breast:

Variant related genes	Relation type
IMPA2	TF binding region
ENSG00000266955	TF binding region
ENSG00000141401	Chromatin interaction
ENSG00000267079	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11660567	0.81[ASN][1000 genomes]
rs16976887	0.88[ASN][1000 genomes]
rs28475846	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28499558	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28509217	0.88[ASN][1000 genomes]
rs28548932	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4239304	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56364728	0.88[ASN][1000 genomes]
rs57967783	0.88[ASN][1000 genomes]
rs58556096	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59796048	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59889312	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6505700	0.88[ASN][1000 genomes]
rs6505701	0.88[ASN][1000 genomes]
rs67450563	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67932171	0.88[ASN][1000 genomes]
rs7230346	0.88[ASN][1000 genomes]
rs7240032	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244678	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72871698	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72871700	0.88[ASN][1000 genomes]
rs72871702	0.88[ASN][1000 genomes]
rs72873509	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72873510	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7407928	0.88[ASN][1000 genomes]
rs7506045	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9973177	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-11995800	Weak transcription	Thymus	Thymus
3	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
4	chr18:11989600-11996400	Enhancers	Pancreas	Pancrea
5	chr18:11990600-11995800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr18:11991000-11999200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr18:11993200-11996600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:11993200-11996600	Enhancers	HSMMtube	muscle
9	chr18:11993200-11998000	Enhancers	Stomach Mucosa	stomach
10	chr18:11993200-11998400	Enhancers	Fetal Muscle Trunk	muscle
11	chr18:11993400-11995800	Enhancers	Lung	lung
12	chr18:11993400-11996400	Enhancers	Placenta	Placenta
13	chr18:11993400-11999400	Enhancers	Fetal Muscle Leg	muscle
14	chr18:11993400-12016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr18:11993600-11996000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr18:11993600-11996000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr18:11993600-11996000	Enhancers	Fetal Intestine Large	intestine
18	chr18:11993600-11996200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr18:11993600-11996200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr18:11993800-11996400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:11993800-11996400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr18:11994000-11996000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr18:11994200-11995800	Enhancers	Osteobl	bone
24	chr18:11994200-11996000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr18:11994200-11996000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr18:11994200-11996000	Flanking Active TSS	A549	lung
27	chr18:11994200-11996000	Enhancers	HSMM	muscle
28	chr18:11994200-11996600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr18:11994400-11996000	Enhancers	Fetal Lung	lung
30	chr18:11994400-11996000	Enhancers	Right Ventricle	heart
31	chr18:11994400-11996000	Flanking Active TSS	HepG2	liver
32	chr18:11994400-11996000	Enhancers	HMEC	breast
33	chr18:11994400-11996000	Enhancers	NHDF-Ad	bronchial
34	chr18:11994400-11996200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr18:11994400-11996200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr18:11994400-11997600	Enhancers	Colonic Mucosa	Colon
37	chr18:11994600-11995800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr18:11994600-11996000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:11994600-11996000	Enhancers	Left Ventricle	heart
40	chr18:11994600-11996000	Enhancers	NHLF	lung
41	chr18:11994600-11996600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr18:11994600-11996800	Enhancers	Liver	Liver
43	chr18:11994600-11996800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr18:11994800-11995800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr18:11994800-11996000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr18:11994800-11996000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr18:11994800-11996000	Enhancers	Right Atrium	heart
48	chr18:11994800-11996000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr18:11994800-11997000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr18:11995000-11996000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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