Variant report

Variant	rs12097707
Chromosome Location	chr1:47799415-47799416
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:374)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:374 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:47799110-47800655	A549	lung:	n/a	n/a
2	TAF1	chr1:47799071-47799651	GM12878	blood:	n/a	n/a
3	NFATC1	chr1:47799146-47799505	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:47798998-47800635	U87	brain:	n/a	n/a
5	POLR2A	chr1:47799145-47800659	GM18526	blood:	n/a	n/a
6	SIN3AK20	chr1:47799255-47799706	K562	blood:	n/a	n/a
7	ELF1	chr1:47799210-47800732	GM12878	blood:	n/a	chr1:47799438-47799447 chr1:47800492-47800505
8	CTCF	chr1:47799300-47799450	GM12869	blood:	n/a	n/a
9	EP300	chr1:47799079-47800686	ECC-1	luminal epithelium:	n/a	chr1:47799439-47799448 chr1:47799973-47799982 chr1:47800605-47800619
10	POLR2A	chr1:47799186-47800037	A549	lung:	n/a	n/a
11	MAZ	chr1:47799087-47800562	GM12878	blood:	n/a	n/a
12	REST	chr1:47799190-47799483	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr1:47799179-47799457	IMR90	lung:	n/a	n/a
14	POLR2A	chr1:47799134-47800651	GM19193	blood:	n/a	n/a
15	SIN3A	chr1:47799099-47799765	GM12878	blood:	n/a	n/a
16	MYC	chr1:47798986-47800526	MCF10A-Er-Src	breast:	n/a	n/a
17	RELA	chr1:47799177-47800684	GM18951	blood:	n/a	n/a
18	POLR2A	chr1:47799149-47800035	Gliobla	brain:	n/a	n/a
19	ATF3	chr1:47799209-47800227	K562	blood:	n/a	n/a
20	POLR2A	chr1:47799005-47800700	GM12892	blood:	n/a	n/a
21	ELF1	chr1:47799186-47800513	GM12878	blood:	n/a	chr1:47799438-47799447 chr1:47800492-47800505
22	RAD21	chr1:47799160-47799482	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:47799134-47801033	K562	blood:	n/a	n/a
24	TAF1	chr1:47798955-47799732	ECC-1	luminal epithelium:	n/a	n/a
25	REST	chr1:47798952-47800214	H1-neurons	neurons:	n/a	n/a
26	HMGN3	chr1:47798972-47800573	K562	blood:	n/a	n/a
27	ZBTB33	chr1:47799257-47799521	HCT-116	colon:	n/a	n/a
28	POLR2A	chr1:47799201-47799517	H1-hESC	embryonic stem cell:	n/a	n/a
29	PML	chr1:47798980-47800768	GM12878	blood:	n/a	n/a
30	EBF1	chr1:47799238-47799516	GM12878	blood:	n/a	n/a
31	MAX	chr1:47798592-47800562	K562	blood:	n/a	n/a
32	POLR2A	chr1:47799167-47800528	GM12878	blood:	n/a	n/a
33	SMC3	chr1:47799294-47799831	K562	blood:	n/a	n/a
34	POLR2A	chr1:47799217-47800013	A549	lung:	n/a	n/a
35	CTCF	chr1:47799300-47799450	WERI-Rb-1	eye:	n/a	n/a
36	MXI1	chr1:47798654-47800794	GM12878	blood:	n/a	n/a
37	FOXP2	chr1:47799291-47800058	PFSK-1	brain:	n/a	n/a
38	TAF1	chr1:47799084-47800613	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr1:47799043-47800659	HCT-116	colon:	n/a	n/a
40	MYC	chr1:47799249-47799501	MCF-7	breast:	n/a	n/a
41	REST	chr1:47799221-47799485	A549	lung:	n/a	n/a
42	YY1	chr1:47799186-47800140	ECC-1	luminal epithelium:	n/a	chr1:47799438-47799447
43	POLR2A	chr1:47798992-47800725	U87	brain:	n/a	n/a
44	POLR2A	chr1:47799127-47800730	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr1:47798943-47800660	K562	blood:	n/a	n/a
46	POLR2A	chr1:47798627-47800735	K562	blood:	n/a	n/a
47	POLR2A	chr1:47798995-47800575	HL-60	blood:	n/a	n/a
48	POLR2A	chr1:47799071-47799988	PANC-1	pancreas:	n/a	n/a
49	GABPA	chr1:47799259-47799552	H1-hESC	embryonic stem cell:	n/a	n/a
50	TAL1	chr1:47799224-47799437	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47748903..47750485-chr1:47798676..47800634,2	K562	blood:
2	chr1:47778595..47781681-chr1:47798356..47800996,6	MCF-7	breast:
3	chr1:47655819..47657436-chr1:47799137..47801227,2	K562	blood:
4	chr1:47799238..47800011-chr17:62503172..62503867,2	Hela-S3	cervix:
5	chr1:28562421..28563279-chr1:47799111..47799932,2	NB4	blood:
6	chr1:47654478..47656007-chr1:47798811..47801587,2	MCF-7	breast:
7	chr1:47772551..47781833-chr1:47797933..47806586,42	K562	blood:
8	chr1:47132421..47133961-chr1:47797739..47800236,2	K562	blood:
9	chr1:47799071..47799830-chr11:62608965..62609651,2	Hela-S3	cervix:
10	chr1:47696136..47700063-chr1:47798634..47802913,8	K562	blood:
11	chr1:47798883..47799427-chr15:42091723..42092546,2	NB4	blood:
12	chr1:47647073..47651610-chr1:47798272..47801392,5	K562	blood:
13	chr1:47696333..47699229-chr1:47798340..47801363,4	K562	blood:
14	chr1:47799038..47799571-chr6:30584746..30585308,2	Hela-S3	cervix:
15	chr1:47798870..47799813-chr5:10307130..10307968,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
CMPK1	TF binding region
ENSG00000130770	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000123472	Chromatin interaction
ENSG00000164237	Chromatin interaction
ENSG00000162367	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000162366	Chromatin interaction
ENSG00000123473	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11211493	1.00[AMR][1000 genomes]
rs11211518	1.00[AMR][1000 genomes]
rs12057442	1.00[AMR][1000 genomes]
rs12061831	1.00[AMR][1000 genomes]
rs12094830	1.00[AMR][1000 genomes]
rs58921777	1.00[AMR][1000 genomes]
rs59984926	1.00[AMR][1000 genomes]
rs6682932	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72894542	1.00[AMR][1000 genomes]
rs72894554	1.00[AMR][1000 genomes]
rs72894556	1.00[AMR][1000 genomes]
rs72894561	1.00[AMR][1000 genomes]
rs72894566	1.00[AMR][1000 genomes]
rs72894577	1.00[AMR][1000 genomes]
rs72896510	1.00[AMR][1000 genomes]
rs72896513	1.00[AMR][1000 genomes]
rs7545862	1.00[AMR][1000 genomes]
rs9436428	1.00[AMR][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	esv3390574	chr1:47778981-47803091	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3380025	chr1:47798390-47801238	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47798200-47800800	Active TSS	A549	lung
2	chr1:47798200-47801000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:47798400-47800600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:47798400-47801000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:47798600-47800600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:47798600-47800600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:47798600-47800600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:47798600-47800800	Active TSS	Esophagus	oesophagus
9	chr1:47798600-47800800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:47798600-47801000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:47798600-47801200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:47798800-47800400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:47798800-47800400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:47798800-47800400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:47798800-47800600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:47798800-47800600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:47798800-47800600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:47798800-47800600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:47798800-47800600	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:47798800-47800600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:47798800-47800600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:47798800-47800600	Active TSS	Colon Smooth Muscle	Colon
23	chr1:47798800-47800600	Active TSS	Ovary	ovary
24	chr1:47798800-47800600	Active TSS	Osteobl	bone
25	chr1:47798800-47800800	Active TSS	H1 Cell Line	embryonic stem cell
26	chr1:47798800-47800800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:47798800-47800800	Active TSS	Left Ventricle	heart
28	chr1:47798800-47800800	Active TSS	Placenta Amnion	Placenta Amnion
29	chr1:47798800-47800800	Active TSS	HSMMtube	muscle
30	chr1:47798800-47800800	Active TSS	NHDF-Ad	bronchial
31	chr1:47798800-47801000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:47798800-47801000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:47798800-47801000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:47798800-47801000	Active TSS	Thymus	Thymus
35	chr1:47798800-47801200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr1:47798800-47801200	Active TSS	HSMM	muscle
37	chr1:47799000-47799600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr1:47799000-47800200	Active TSS	Fetal Muscle Trunk	muscle
39	chr1:47799000-47800400	Active TSS	Brain Cingulate Gyrus	brain
40	chr1:47799000-47800400	Active TSS	Brain Hippocampus Middle	brain
41	chr1:47799000-47800400	Active TSS	Fetal Muscle Leg	muscle
42	chr1:47799000-47800400	Active TSS	Placenta	Placenta
43	chr1:47799000-47800400	Active TSS	Fetal Stomach	stomach
44	chr1:47799000-47800400	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:47799000-47800400	Bivalent/Poised TSS	HepG2	liver
46	chr1:47799000-47800400	Active TSS	NHLF	lung
47	chr1:47799000-47800600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:47799000-47800600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:47799000-47800600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:47799000-47800600	Active TSS	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links