Variant report

Variant	rs12140021
Chromosome Location	chr1:151809530-151809531
allele	C/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	TCF7L2	chr1:151809018-151809922	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:151809002-151809604	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr1:151809380-151809530	AoAF	blood vessel:	n/a	n/a
4	NR2F2	chr1:151808672-151810171	MCF-7	breast:	n/a	n/a
5	EP300	chr1:151809403-151809628	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr1:151809011-151809776	ECC-1	luminal epithelium:	n/a	chr1:151809368-151809375 chr1:151809105-151809112
7	CTCF	chr1:151808347-151809619	SK-N-SH	brain:	n/a	chr1:151808816-151808829 chr1:151809084-151809105 chr1:151809091-151809104 chr1:151809095-151809104 chr1:151809089-151809107 chr1:151809598-151809611
8	MAX	chr1:151808870-151809747	Hela-S3	cervix:	n/a	n/a
9	GATA3	chr1:151808902-151809829	T-47D	breast:	n/a	chr1:151809442-151809452
10	TFAP2A	chr1:151808935-151809637	Hela-S3	cervix:	n/a	chr1:151809125-151809140 chr1:151809126-151809137
11	NFIC	chr1:151808690-151809959	ECC-1	luminal epithelium:	n/a	n/a
12	SMC3	chr1:151808827-151809864	Hela-S3	cervix:	n/a	chr1:151809488-151809498 chr1:151809091-151809105
13	MYC	chr1:151809422-151809556	MCF-7	breast:	n/a	n/a
14	TFAP2C	chr1:151808963-151809606	Hela-S3	cervix:	n/a	chr1:151809125-151809140
15	USF2	chr1:151809428-151809841	Hela-S3	cervix:	n/a	n/a
16	SPI1	chr1:151808816-151809601	HL-60	blood:	n/a	chr1:151809443-151809456 chr1:151809163-151809176
17	RCOR1	chr1:151808943-151809880	Hela-S3	cervix:	n/a	n/a
18	SMC3	chr1:151808258-151809706	SK-N-SH	brain:	n/a	chr1:151809488-151809498 chr1:151809091-151809105
19	CTCF	chr1:151809420-151809570	GM12878	blood:	n/a	n/a
20	MAZ	chr1:151808963-151809857	Hela-S3	cervix:	n/a	n/a
21	BRCA1	chr1:151808884-151809800	Hela-S3	cervix:	n/a	n/a
22	RAD21	chr1:151808714-151809824	MCF-7	breast:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104 chr1:151809598-151809612
23	GTF2F1	chr1:151808950-151809618	Hela-S3	cervix:	n/a	n/a
24	MXI1	chr1:151808967-151809714	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr1:151808822-151809829	Hela-S3	cervix:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151809087-151809106 chr1:151809090-151809104 chr1:151809598-151809612
26	RFX5	chr1:151808931-151809631	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr1:151808306-151809793	MCF-7	breast:	n/a	chr1:151808816-151808829 chr1:151809084-151809105 chr1:151809091-151809104 chr1:151809095-151809104 chr1:151809089-151809107 chr1:151809598-151809611
28	RAD21	chr1:151808602-151809609	HCT-116	colon:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104
29	MAX	chr1:151808908-151809612	Hela-S3	cervix:	n/a	n/a
30	TBP	chr1:151809392-151809578	Hela-S3	cervix:	n/a	n/a
31	CHD2	chr1:151809015-151809788	Hela-S3	cervix:	n/a	chr1:151809583-151809593 chr1:151809668-151809678
32	ZNF217	chr1:151808979-151809749	MCF-7	breast:	n/a	n/a
33	RAD21	chr1:151808601-151809579	HCT-116	colon:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104
34	FOXA1	chr1:151809328-151809724	T-47D	breast:	n/a	n/a
35	MAX	chr1:151808621-151810142	MCF-7	breast:	n/a	n/a
36	MYC	chr1:151808907-151809880	Hela-S3	cervix:	n/a	n/a
37	GABPA	chr1:151808730-151810259	MCF-7	breast:	n/a	n/a
38	MAFK	chr1:151808943-151809667	Hela-S3	cervix:	n/a	chr1:151809439-151809454 chr1:151809526-151809543
39	RAD21	chr1:151808555-151809699	MCF-7	breast:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104 chr1:151809598-151809612
40	MAX	chr1:151808826-151809955	MCF-7	breast:	n/a	n/a
41	MYC	chr1:151808931-151809625	MCF10A-Er-Src	breast:	n/a	n/a
42	CEBPB	chr1:151808933-151809820	Hela-S3	cervix:	n/a	n/a
43	FOS	chr1:151808953-151809668	Hela-S3	cervix:	n/a	chr1:151809530-151809539
44	NFIC	chr1:151808919-151809813	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151510584..151515702-chr1:151808389..151812312,7	MCF-7	breast:
2	chr1:151735784..151737318-chr1:151808411..151810675,2	MCF-7	breast:
3	chr1:151712042..151713073-chr1:151808628..151809658,5	MCF-7	breast:
4	chr1:151483121..151485992-chr1:151808020..151810121,3	MCF-7	breast:
5	chr1:151707202..151708163-chr1:151808657..151809536,5	MCF-7	breast:
6	chr1:151804539..151806807-chr1:151808292..151812161,4	K562	blood:
7	chr1:19410890..19413871-chr1:151808457..151811077,2	MCF-7	breast:
8	chr1:151773064..151773919-chr1:151809447..151809983,2	MCF-7	breast:
9	chr1:151808928..151809951-chr1:151853655..151854418,3	MCF-7	breast:
10	chr1:151808355..151810594-chr1:151852540..151855427,2	MCF-7	breast:
11	chr1:151734307..151737224-chr1:151809345..151813879,7	MCF-7	breast:
12	chr1:151809106..151809860-chr3:64016088..64016677,2	MCF-7	breast:
13	chr1:151809121..151809703-chr4:128801479..128802412,2	Hela-S3	cervix:
14	chr1:151808934..151809634-chr1:151853928..151854568,2	MCF-7	breast:
15	chr1:151717253..151722089-chr1:151808382..151812448,4	MCF-7	breast:
16	chr1:151764210..151765820-chr1:151809530..151811612,2	MCF-7	breast:
17	chr1:151566525..151567546-chr1:151808737..151809625,3	MCF-7	breast:
18	chr1:151566301..151567308-chr1:151808522..151809558,4	K562	blood:
19	chr1:151808068..151810311-chr1:151964159..151966593,4	MCF-7	breast:
20	chr1:151430044..151432386-chr1:151809146..151811411,2	MCF-7	breast:
21	chr1:151795525..151798477-chr1:151809091..151811611,2	MCF-7	breast:
22	chr1:151807915..151809581-chr1:151880993..151883384,2	MCF-7	breast:
23	chr1:151678020..151678605-chr1:151808685..151809547,3	MCF-7	breast:
24	chr1:151506889..151507829-chr1:151808656..151809532,4	K562	blood:
25	chr1:151507235..151508171-chr1:151808641..151809567,3	MCF-7	breast:
26	chr1:151809368..151811108-chr1:151856031..151858705,2	MCF-7	breast:
27	chr1:151416014..151416766-chr1:151808595..151809606,5	K562	blood:

Variant related genes	Relation type
ENSG00000234614	TF binding region
ENSG00000232536	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000142731	Chromatin interaction
ENSG00000206980	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10888438	0.87[ASN][1000 genomes]
rs10888439	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204899	0.87[EUR][1000 genomes]
rs11204900	0.83[EUR][1000 genomes]
rs11204901	0.84[EUR][1000 genomes]
rs6667460	0.85[ASN][1000 genomes]
rs7536659	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7544269	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1804657	chr1:151784152-151825756	Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151802400-151810400	Weak transcription	Right Atrium	heart
2	chr1:151802800-151811000	Enhancers	Placenta	Placenta
3	chr1:151804400-151810200	Weak transcription	Gastric	stomach
4	chr1:151804400-151810600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:151804600-151812000	Enhancers	Pancreas	Pancrea
6	chr1:151805000-151810200	Weak transcription	Right Ventricle	heart
7	chr1:151805200-151810400	Weak transcription	Lung	lung
8	chr1:151805200-151810600	Enhancers	Dnd41	blood
9	chr1:151805400-151810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:151805600-151809800	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:151805600-151811200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:151805800-151809600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:151806000-151810400	Weak transcription	Esophagus	oesophagus
14	chr1:151806200-151810400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:151806200-151811000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:151806400-151811800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:151806800-151810000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:151807000-151810800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:151807200-151809600	Enhancers	HepG2	liver
20	chr1:151807200-151810600	Enhancers	Liver	Liver
21	chr1:151808200-151810400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:151808400-151809600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:151808400-151809600	Enhancers	Fetal Intestine Large	intestine
24	chr1:151808400-151810000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr1:151808400-151810400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:151808400-151810400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
27	chr1:151808400-151810800	Enhancers	HMEC	breast
28	chr1:151808600-151809600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:151808600-151809600	Enhancers	Fetal Intestine Small	intestine
30	chr1:151808600-151809800	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:151808600-151810400	Enhancers	NHEK	skin
32	chr1:151808800-151809600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr1:151808800-151809800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr1:151808800-151810000	Enhancers	A549	lung
35	chr1:151808800-151810200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr1:151808800-151810200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr1:151808800-151810400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:151808800-151810400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:151808800-151810800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:151808800-151810800	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr1:151808800-151811200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:151809000-151809800	Enhancers	Primary T cells from cord blood	blood
43	chr1:151809000-151810000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:151809000-151810200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:151809000-151810200	Flanking Active TSS	Hela-S3	cervix
46	chr1:151809000-151812000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr1:151809200-151809600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:151809200-151809600	Enhancers	Colonic Mucosa	Colon
49	chr1:151809200-151809600	Enhancers	Thymus	Thymus
50	chr1:151809200-151809800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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