Variant report

Variant	rs3810000
Chromosome Location	chr18:29523096-29523097
allele	A/G
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	POLR2A	chr18:29522074-29524311	GM12878	blood:	n/a	n/a
2	YY1	chr18:29522583-29523253	H1-hESC	embryonic stem cell:	n/a	chr18:29522740-29522754 chr18:29523047-29523057 chr18:29523047-29523069 chr18:29522746-29522755 chr18:29523050-29523058
3	GABPA	chr18:29522867-29523456	SK-N-SH	brain:	n/a	chr18:29523100-29523109
4	YY1	chr18:29522266-29523222	K562	blood:	n/a	chr18:29522740-29522754 chr18:29523047-29523057 chr18:29523047-29523069 chr18:29522746-29522755 chr18:29523050-29523058
5	PML	chr18:29522850-29523229	GM12878	blood:	n/a	n/a
6	USF2	chr18:29522867-29523737	H1-hESC	embryonic stem cell:	n/a	chr18:29523112-29523125 chr18:29523114-29523123 chr18:29523115-29523124 chr18:29523108-29523129 chr18:29523114-29523123 chr18:29523113-29523124
7	SP4	chr18:29522868-29523245	H1-hESC	embryonic stem cell:	n/a	n/a
8	ATF3	chr18:29522818-29523234	H1-hESC	embryonic stem cell:	n/a	chr18:29523114-29523123 chr18:29523103-29523123
9	POLR2A	chr18:29522415-29523796	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr18:29522016-29523663	MCF10A-Er-Src	breast:	n/a	n/a
11	YY1	chr18:29522517-29523612	HepG2	liver:	n/a	chr18:29522740-29522754 chr18:29523047-29523057 chr18:29523047-29523069 chr18:29522746-29522755 chr18:29523050-29523058
12	MAX	chr18:29522858-29523953	SK-N-SH	brain:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
13	YY1	chr18:29522650-29523270	ECC-1	luminal epithelium:	n/a	chr18:29522740-29522754 chr18:29523047-29523057 chr18:29523047-29523069 chr18:29522746-29522755 chr18:29523050-29523058
14	ZBTB33	chr18:29522990-29523237	A549	lung:	n/a	chr18:29523098-29523108
15	ATF2	chr18:29522854-29523220	H1-hESC	embryonic stem cell:	n/a	n/a
16	ELF1	chr18:29522722-29523884	K562	blood:	n/a	chr18:29523206-29523217 chr18:29523207-29523216
17	TAF1	chr18:29522392-29523246	H1-neurons	neurons:	n/a	n/a
18	RFX5	chr18:29522376-29523763	HepG2	liver:	n/a	chr18:29522850-29522866
19	PAX5	chr18:29522844-29523225	GM12878	blood:	n/a	chr18:29523170-29523179
20	E2F6	chr18:29522325-29523876	K562	blood:	n/a	chr18:29523095-29523105 chr18:29522747-29522757 chr18:29522413-29522423
21	POLR2A	chr18:29522017-29524380	HepG2	liver:	n/a	n/a
22	SIX5	chr18:29522928-29523218	A549	lung:	n/a	n/a
23	POLR2A	chr18:29522379-29523808	HEK293	kidney:	n/a	n/a
24	USF1	chr18:29522839-29523245	GM12878	blood:	n/a	chr18:29523112-29523125 chr18:29523114-29523123 chr18:29523115-29523124 chr18:29523108-29523129 chr18:29523114-29523123
25	CREB1	chr18:29522797-29523727	H1-hESC	embryonic stem cell:	n/a	n/a
26	TEAD4	chr18:29522725-29524272	ECC-1	luminal epithelium:	n/a	chr18:29522963-29522972
27	POLR2A	chr18:29522846-29523568	A549	lung:	n/a	n/a
28	EGR1	chr18:29522924-29523561	GM12878	blood:	n/a	chr18:29523095-29523108 chr18:29523280-29523294 chr18:29523208-29523217 chr18:29523095-29523105 chr18:29523262-29523276
29	RCOR1	chr18:29522189-29523842	K562	blood:	n/a	n/a
30	MTA3	chr18:29522729-29523195	GM12878	blood:	n/a	n/a
31	EGR1	chr18:29522941-29523667	MCF-7	breast:	n/a	chr18:29523095-29523108 chr18:29523280-29523294 chr18:29523208-29523217 chr18:29523095-29523105 chr18:29523262-29523276
32	NFE2	chr18:29522945-29523273	GM12878	blood:	n/a	chr18:29523114-29523123
33	TBL1XR1	chr18:29522352-29523710	K562	blood:	n/a	n/a
34	MYC	chr18:29522694-29523866	Hela-S3	cervix:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
35	POLR2A	chr18:29521981-29523799	PBDE	blood:	n/a	n/a
36	POLR2A	chr18:29522072-29523888	GM12891	blood:	n/a	n/a
37	CHD1	chr18:29522247-29523787	GM12878	blood:	n/a	n/a
38	POLR2A	chr18:29522172-29523820	GM15510	blood:	n/a	n/a
39	SIN3A	chr18:29522284-29523836	GM12878	blood:	n/a	chr18:29523115-29523124
40	REST	chr18:29522686-29523267	H1-neurons	neurons:	n/a	n/a
41	RCOR1	chr18:29522633-29523851	GM12878	blood:	n/a	n/a
42	YY1	chr18:29522667-29523227	SK-N-SH_RA	brain:	n/a	chr18:29522740-29522754 chr18:29523047-29523057 chr18:29523047-29523069 chr18:29522746-29522755 chr18:29523050-29523058
43	NFATC1	chr18:29522718-29523268	GM12878	blood:	n/a	n/a
44	USF1	chr18:29522751-29523764	ECC-1	luminal epithelium:	n/a	chr18:29523112-29523125 chr18:29523114-29523123 chr18:29523115-29523124 chr18:29523108-29523129 chr18:29523114-29523123
45	POLR2A	chr18:29522780-29523217	K562	blood:	n/a	n/a
46	TBP	chr18:29522259-29523867	K562	blood:	n/a	n/a
47	TEAD4	chr18:29522815-29523930	ECC-1	luminal epithelium:	n/a	chr18:29522963-29522972
48	MXI1	chr18:29522044-29523995	HepG2	liver:	n/a	n/a
49	EGR1	chr18:29522967-29523616	GM12878	blood:	n/a	chr18:29523095-29523108 chr18:29523280-29523294 chr18:29523208-29523217 chr18:29523095-29523105 chr18:29523262-29523276
50	POLR2A	chr18:29522128-29523810	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr18:29523063-29523113	Caco-2	colon:	n/a
2	chr18:29523063-29523113	PFSK-1	brain:	n/a
3	chr18:29523063-29523113	ovcar-3	ovarian:	n/a
4	chr18:29523063-29523113	AG04450	lung:	fetal
5	chr18:29523078-29523128	HRPEpiC	eye:	n/a
6	chr18:29523078-29523128	HMEC	breast:	n/a
7	chr18:29523078-29523128	CMK	blood:	n/a
8	chr18:29523063-29523113	HAEpiC	amniotic membrane:	n/a
9	chr18:29523078-29523128	HCM	heart:	n/a
10	chr18:29523063-29523113	RPTEC	kidney:	n/a
11	chr18:29523063-29523113	Hepatocyte	liver:	n/a
12	chr18:29523063-29523113	HRPEpiC	eye:	n/a
13	chr18:29523063-29523113	HRCEpiC	kidney:	n/a
14	chr18:29523063-29523113	CMK	blood:	n/a
15	chr18:29523063-29523113	U87	brain:	n/a
16	chr18:29523078-29523128	LNCaP	prostate:	n/a
17	chr18:29523063-29523113	HCPEpiC	choroid plexus:	n/a
18	chr18:29523063-29523113	A549	lung:	n/a
19	chr18:29523078-29523128	AG10803	skin:	n/a
20	chr18:29523063-29523113	HCF	heart:	n/a
21	chr18:29523078-29523128	HNPCEpiC	eye:	n/a
22	chr18:29523078-29523128	NB4	blood:	n/a
23	chr18:29523078-29523128	AoSMC	blood vessel:	n/a
24	chr18:29523063-29523113	HNPCEpiC	eye:	n/a
25	chr18:29523078-29523128	AG09319	gingival:	n/a
26	chr18:29523063-29523113	MCF10A-Er-Src	breast:	n/a
27	chr18:29523063-29523113	GM12878	blood:	n/a
28	chr18:29523078-29523128	A549	lung:	n/a
29	chr18:29523078-29523128	GM06990	blood:	n/a
30	chr18:29523078-29523128	AG09309	skin:	n/a
31	chr18:29523078-29523128	GM19239	blood:	n/a
32	chr18:29523078-29523128	MCF10A-Er-Src	breast:	n/a
33	chr18:29523063-29523113	NB4	blood:	n/a
34	chr18:29523078-29523128	GM12878	blood:	n/a
35	chr18:29523063-29523113	K562	blood:	n/a
36	chr18:29523078-29523128	HRE	kidney:	n/a
37	chr18:29523063-29523113	BJ	skin:	n/a
38	chr18:29523063-29523113	HIPEpiC	eye:	n/a
39	chr18:29523063-29523113	NHDF-neo	bronchial:	n/a
40	chr18:29523078-29523128	HIPEpiC	eye:	n/a
41	chr18:29523063-29523113	BE2_C	brain:	n/a
42	chr18:29523078-29523128	NT2-D1	testis:	n/a
43	chr18:29523063-29523113	HMEC	breast:	n/a
44	chr18:29523078-29523128	HepG2	liver:	n/a
45	chr18:29523063-29523113	AG09309	skin:	n/a
46	chr18:29523078-29523128	Hela-S3	cervix:	n/a
47	chr18:29523078-29523128	AG04450	lung:	fetal
48	chr18:29523078-29523128	HCT-116	colon:	n/a
49	chr18:29523063-29523113	AG10803	skin:	n/a
50	chr18:29523078-29523128	SK-N-SH_RA	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:29517111..29520943-chr18:29521139..29523956,5	MCF-7	breast:
2	chr18:29522249..29524505-chr18:29596603..29599089,2	MCF-7	breast:
3	chr18:29521939..29525237-chr18:29670716..29673913,4	MCF-7	breast:
4	chr17:48942638..48944565-chr18:29522050..29524653,2	MCF-7	breast:
5	chr18:29518719..29521005-chr18:29521192..29525426,5	MCF-7	breast:
6	chr18:29450429..29452203-chr18:29521687..29523259,2	MCF-7	breast:
7	chr18:29521665..29524441-chr18:29544834..29547590,2	K562	blood:
8	chr18:29522696..29523369-chr18:29598378..29599258,2	Hela-S3	cervix:
9	chr18:29521618..29525019-chr18:29670361..29672184,4	MCF-7	breast:
10	chr1:230202892..230203511-chr18:29522624..29523602,2	HCT-116	colon:
11	chr18:29521522..29523729-chr18:29672844..29674625,2	MCF-7	breast:
12	chr18:29521537..29525393-chr18:29670839..29674328,7	K562	blood:
13	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:
14	chr18:29468408..29471507-chr18:29523062..29524905,3	K562	blood:
15	chr18:29520544..29523172-chr18:33708356..33710539,2	K562	blood:
16	chr1:154155258..154156060-chr18:29522614..29523350,2	Hela-S3	cervix:

Variant related genes	Relation type
TRAPPC8	TF binding region
TRAPPC8	CpG island
ENSG00000143641	Chromatin interaction
ENSG00000265008	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000134759	Chromatin interaction
ENSG00000238982	Chromatin interaction
ENSG00000263917	Chromatin interaction
ENSG00000222320	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000141424	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000153339	Chromatin interaction
ENSG00000101695	Chromatin interaction
ENSG00000266105	Chromatin interaction
ENSG00000134758	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12604916	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12604977	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12605853	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276143	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59301557	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr18:29520200-29526800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:29521000-29524400	Active TSS	Psoas Muscle	Psoas
3	chr18:29521200-29524200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr18:29521200-29524400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr18:29521200-29524400	Active TSS	GM12878-XiMat	blood
6	chr18:29521200-29524800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr18:29521200-29524800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr18:29521200-29525200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr18:29521400-29523600	Active TSS	Muscle Satellite Cultured Cells	--
10	chr18:29521400-29524000	Active TSS	Ovary	ovary
11	chr18:29521400-29524000	Active TSS	NHDF-Ad	bronchial
12	chr18:29521400-29524000	Active TSS	NHLF	lung
13	chr18:29521400-29524200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr18:29521400-29524200	Active TSS	HSMM	muscle
15	chr18:29521400-29524400	Active TSS	Fetal Kidney	kidney
16	chr18:29521400-29524600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:29521400-29524600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr18:29521400-29525000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr18:29521400-29525400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr18:29521600-29523400	Active TSS	Colonic Mucosa	Colon
21	chr18:29521600-29523600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr18:29521600-29523800	Active TSS	Thymus	Thymus
23	chr18:29521600-29524000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr18:29521600-29524000	Active TSS	Aorta	Aorta
25	chr18:29521600-29524000	Active TSS	Fetal Intestine Small	intestine
26	chr18:29521600-29524200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr18:29521600-29524200	Active TSS	Fetal Intestine Large	intestine
28	chr18:29521600-29524200	Active TSS	Right Ventricle	heart
29	chr18:29521600-29524200	Active TSS	A549	lung
30	chr18:29521600-29524800	Active TSS	H1 Cell Line	embryonic stem cell
31	chr18:29521600-29524800	Active TSS	HSMMtube	muscle
32	chr18:29521600-29525400	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr18:29521800-29523600	Active TSS	Placenta	Placenta
34	chr18:29521800-29523800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr18:29521800-29523800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr18:29521800-29524000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr18:29521800-29524000	Active TSS	Fetal Heart	heart
38	chr18:29521800-29524000	Active TSS	K562	blood
39	chr18:29521800-29524200	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr18:29521800-29524200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr18:29521800-29524400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr18:29521800-29524400	Active TSS	Fetal Muscle Trunk	muscle
43	chr18:29521800-29524600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr18:29521800-29524600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr18:29522000-29523200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr18:29522000-29523400	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr18:29522000-29523400	Active TSS	HMEC	breast
48	chr18:29522000-29523400	Active TSS	NH-A	brain
49	chr18:29522000-29523400	Active TSS	NHEK	skin
50	chr18:29522000-29523600	Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links