Variant report

Variant	rs74127540
Chromosome Location	chr1:151128785-151128786
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	RAD21	chr1:151128415-151128906	HepG2	liver:	n/a	chr1:151128647-151128666 chr1:151128650-151128663
2	WRNIP1	chr1:151128554-151128824	GM12878	blood:	n/a	n/a
3	CTCF	chr1:151128544-151128796	Fibrobl	skin:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
4	CTCF	chr1:151128556-151128821	HepG2	liver:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
5	FOXM1	chr1:151128421-151128893	GM12878	blood:	n/a	n/a
6	ZMIZ1	chr1:151128546-151128958	K562	blood:	n/a	n/a
7	RAD21	chr1:151128525-151128900	ECC-1	luminal epithelium:	n/a	chr1:151128647-151128666 chr1:151128650-151128663
8	CTCF	chr1:151128534-151128800	Kidney_OC	kidney:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
9	CTCF	chr1:151128353-151128872	HCT-116	colon:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
10	CTCF	chr1:151128700-151128850	WI-38	lung:	n/a	n/a
11	CTCF	chr1:151128529-151128811	GM12891	blood:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
12	CTCF	chr1:151128530-151128816	GM12878	blood:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
13	SMC3	chr1:151128249-151128997	SK-N-SH	brain:	n/a	chr1:151128651-151128665 chr1:151128657-151128665
14	ZNF263	chr1:151128549-151129036	HEK293-T-REx	kidney:	n/a	chr1:151128698-151128707
15	RAD21	chr1:151128484-151128838	A549	lung:	n/a	chr1:151128647-151128666 chr1:151128650-151128663
16	CTCF	chr1:151128535-151128806	MCF-7	breast:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
17	CTCF	chr1:151128533-151128814	MCF-7	breast:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
18	CTCF	chr1:151128526-151128829	H1-hESC	embryonic stem cell:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
19	CTCF	chr1:151128483-151128905	A549	lung:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
20	CTCF	chr1:151128528-151128809	LNCaP	prostate:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
21	CTCF	chr1:151128520-151128813	NHEK	skin:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
22	CTCF	chr1:151128521-151128841	Spleen_OC	spleen:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
23	RAD21	chr1:151128453-151128872	HepG2	liver:	n/a	chr1:151128647-151128666 chr1:151128650-151128663
24	CTCF	chr1:151128526-151128814	HUVEC	blood vessel:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
25	ZNF384	chr1:151128177-151129229	GM12878	blood:	n/a	n/a
26	CTCF	chr1:151128503-151128880	T-47D	breast:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
27	CTCF	chr1:151128468-151128854	K562	blood:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
28	POLR2A	chr1:151128606-151128942	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr1:151128535-151128804	IMR90	lung:	n/a	n/a
30	MAX	chr1:151128512-151130130	NB4	blood:	n/a	chr1:151129937-151129947
31	RAD21	chr1:151128294-151129144	SK-N-SH	brain:	n/a	chr1:151128647-151128666 chr1:151128650-151128663
32	STAT1	chr1:151128627-151129150	GM12878	blood:	n/a	chr1:151128699-151128707 chr1:151128970-151128977
33	NFIC	chr1:151128495-151129281	GM12878	blood:	n/a	n/a
34	CTCF	chr1:151128542-151128795	LNCaP	prostate:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
35	CTCF	chr1:151128516-151128816	Lung_OC	lung:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
36	RAD21	chr1:151128438-151128925	H1-hESC	embryonic stem cell:	n/a	chr1:151128647-151128666 chr1:151128650-151128663
37	JUND	chr1:151128558-151128801	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr1:151128544-151128831	GM10266	blood:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
39	CTCF	chr1:151128518-151128820	GM19238	blood:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
40	CTCF	chr1:151128527-151128851	A549	lung:	n/a	chr1:151128644-151128665 chr1:151128651-151128664 chr1:151128656-151128664 chr1:151128649-151128667
41	ZNF143	chr1:151128503-151128834	K562	blood:	n/a	n/a
42	MTA3	chr1:151128534-151130344	GM12878	blood:	n/a	n/a
43	RAD21	chr1:151128522-151128933	ECC-1	luminal epithelium:	n/a	chr1:151128647-151128666 chr1:151128650-151128663
44	MAZ	chr1:151128508-151128830	K562	blood:	n/a	n/a
45	ZKSCAN1	chr1:151128522-151128808	Hela-S3	cervix:	n/a	n/a
46	RFX5	chr1:151128537-151128808	Hela-S3	cervix:	n/a	n/a
47	RAD21	chr1:151128460-151128827	K562	blood:	n/a	chr1:151128647-151128666 chr1:151128650-151128663
48	RCOR1	chr1:151128544-151128833	K562	blood:	n/a	n/a
49	YY1	chr1:151128557-151128791	GM12878	blood:	n/a	n/a
50	BHLHE40	chr1:151128606-151128831	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151116657..151121305-chr1:151127749..151129795,4	K562	blood:
2	chr1:150994233..150997009-chr1:151128495..151131109,2	MCF-7	breast:
3	chr1:150996743..150997725-chr1:151128187..151129096,8	K562	blood:
4	chr1:151042151..151045476-chr1:151127754..151130933,3	MCF-7	breast:
5	chr1:151029085..151030756-chr1:151127218..151129081,2	MCF-7	breast:
6	chr1:151043249..151044250-chr1:151127996..151129187,6	MCF-7	breast:
7	chr1:151128359..151130289-chr1:151160585..151164269,3	K562	blood:
8	chr1:151030606..151033424-chr1:151127257..151129173,3	MCF-7	breast:
9	chr1:151071447..151073068-chr1:151128034..151129071,15	MCF-7	breast:
10	chr1:150997070..150998682-chr1:151128410..151130437,2	K562	blood:
11	chr1:151041073..151043333-chr1:151126816..151129566,2	K562	blood:
12	chr1:151128133..151130862-chr1:151227086..151228869,2	MCF-7	breast:
13	chr1:151114895..151122057-chr1:151125026..151130825,9	MCF-7	breast:
14	chr1:151043769..151044429-chr1:151128275..151128862,2	MCF-7	breast:
15	chr1:150996742..150997632-chr1:151128159..151129154,8	MCF-7	breast:
16	chr1:151117604..151120749-chr1:151128246..151131666,4	MCF-7	breast:
17	chr1:150978801..150979511-chr1:151128274..151129125,2	MCF-7	breast:
18	chr1:150997162..150997937-chr1:151128073..151128968,3	MCF-7	breast:
19	chr1:150980779..150982400-chr1:151127994..151130267,2	MCF-7	breast:
20	chr1:151107806..151108623-chr1:151128265..151128961,2	K562	blood:
21	chr1:151128026..151130888-chr1:151138043..151140258,2	MCF-7	breast:

Variant related genes	Relation type
SCNM1	TF binding region
TNFAIP8L2	TF binding region
ENSG00000159352	Chromatin interaction
ENSG00000200759	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163156	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs41299635	1.00[AMR][1000 genomes]
rs41310891	1.00[AMR][1000 genomes]
rs55716130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55935377	1.00[AMR][1000 genomes]
rs57330524	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58618837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58763463	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59737164	1.00[AMR][1000 genomes]
rs60636837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60865304	1.00[AMR][1000 genomes]
rs74125051	1.00[AMR][1000 genomes]
rs74125053	1.00[AMR][1000 genomes]
rs74125059	1.00[AMR][1000 genomes]
rs74125062	1.00[AMR][1000 genomes]
rs74125063	1.00[AMR][1000 genomes]
rs74125065	1.00[AMR][1000 genomes]
rs74125077	1.00[AMR][1000 genomes]
rs74125079	1.00[AMR][1000 genomes]
rs74125080	1.00[AMR][1000 genomes]
rs74125087	1.00[AMR][1000 genomes]
rs74125088	1.00[AMR][1000 genomes]
rs74125093	1.00[AMR][1000 genomes]
rs74127505	1.00[AMR][1000 genomes]
rs74127506	1.00[AMR][1000 genomes]
rs74127513	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127514	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127515	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127528	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127529	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127530	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127531	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127535	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127537	0.82[AFR][1000 genomes]
rs74127539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151120000-151128800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:151120000-151129200	Weak transcription	Aorta	Aorta
3	chr1:151120000-151130800	Weak transcription	Pancreas	Pancrea
4	chr1:151120000-151131200	Weak transcription	Ovary	ovary
5	chr1:151120000-151131400	Weak transcription	NH-A	brain
6	chr1:151120000-151131400	Weak transcription	NHLF	lung
7	chr1:151120200-151128800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:151120200-151128800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:151120200-151128800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:151120200-151129000	Weak transcription	Esophagus	oesophagus
11	chr1:151120200-151129400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:151120200-151129400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:151120200-151129400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:151120200-151129400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:151120200-151129600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:151120200-151129800	Weak transcription	Fetal Lung	lung
17	chr1:151120200-151130800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:151120200-151131000	Weak transcription	Osteobl	bone
19	chr1:151120200-151131200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:151120200-151132000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:151120200-151132000	Weak transcription	NHDF-Ad	bronchial
22	chr1:151120400-151128800	Weak transcription	NHEK	skin
23	chr1:151120400-151129000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:151120400-151129000	Weak transcription	HSMM	muscle
25	chr1:151120400-151129200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:151120400-151129200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:151120400-151129200	Weak transcription	Fetal Brain Female	brain
28	chr1:151120400-151129400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:151120400-151129600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:151120400-151129800	Weak transcription	Fetal Brain Male	brain
31	chr1:151120400-151130200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:151120400-151131600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:151120400-151133200	Weak transcription	Psoas Muscle	Psoas
34	chr1:151120600-151129400	Weak transcription	Fetal Kidney	kidney
35	chr1:151120600-151129800	Weak transcription	Brain Angular Gyrus	brain
36	chr1:151120600-151130800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:151120600-151132000	Weak transcription	HSMMtube	muscle
38	chr1:151121400-151128800	Weak transcription	Fetal Intestine Large	intestine
39	chr1:151122800-151128800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:151123600-151128800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:151125000-151132800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:151125200-151129000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:151125800-151128800	Weak transcription	Stomach Mucosa	stomach
44	chr1:151127000-151130000	Enhancers	HUVEC	blood vessel
45	chr1:151127200-151134600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:151127400-151128800	Strong transcription	Fetal Intestine Small	intestine
47	chr1:151127400-151134800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:151127600-151128800	Enhancers	Primary hematopoietic stem cells	blood
49	chr1:151127600-151129200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:151127600-151129600	Weak transcription	Brain Inferior Temporal Lobe	brain

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