Variant report

Variant	rs607518
Chromosome Location	chr1:150954671-150954672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:117)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:117 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr1:150954074-150955130	HepG2	liver:	n/a	n/a
2	PML	chr1:150953613-150955128	MCF-7	breast:	n/a	n/a
3	MBD4	chr1:150954408-150955137	HepG2	liver:	n/a	n/a
4	RXRA	chr1:150954220-150954801	HepG2	liver:	n/a	chr1:150954570-150954577
5	ZNF217	chr1:150953711-150954952	MCF-7	breast:	n/a	n/a
6	MAX	chr1:150954401-150954855	HepG2	liver:	n/a	n/a
7	HA-E2F1	chr1:150953516-150954874	MCF-7	breast:	n/a	n/a
8	EP300	chr1:150953548-150954677	ECC-1	luminal epithelium:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
9	ESR1	chr1:150954059-150954941	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr1:150953533-150954895	HepG2	liver:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
11	NR2F2	chr1:150953437-150955516	MCF-7	breast:	n/a	n/a
12	HEY1	chr1:150954279-150954981	HepG2	liver:	n/a	n/a
13	MAX	chr1:150953445-150955230	MCF-7	breast:	n/a	chr1:150954010-150954019
14	POLR2A	chr1:150954464-150954935	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr1:150953478-150955152	MCF-7	breast:	n/a	n/a
16	SIN3AK20	chr1:150953436-150955846	MCF-7	breast:	n/a	n/a
17	TEAD4	chr1:150953496-150954733	ECC-1	luminal epithelium:	n/a	n/a
18	NFIC	chr1:150954208-150954755	HepG2	liver:	n/a	n/a
19	FOXA1	chr1:150954499-150954865	T-47D	breast:	n/a	n/a
20	EP300	chr1:150953472-150954827	HepG2	liver:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
21	HNF4G	chr1:150954234-150954853	HepG2	liver:	n/a	n/a
22	ELF1	chr1:150954398-150954784	HepG2	liver:	n/a	n/a
23	MYC	chr1:150954408-150954761	HepG2	liver:	n/a	n/a
24	MAX	chr1:150953420-150955157	HepG2	liver:	n/a	chr1:150954010-150954019
25	USF2	chr1:150954541-150954822	Hela-S3	cervix:	n/a	n/a
26	RCOR1	chr1:150954463-150954856	K562	blood:	n/a	n/a
27	ESR1	chr1:150954027-150954921	ECC-1	luminal epithelium:	n/a	n/a
28	NFIC	chr1:150953644-150955029	ECC-1	luminal epithelium:	n/a	n/a
29	GATA3	chr1:150953803-150954956	MCF-7	breast:	n/a	n/a
30	MXI1	chr1:150954318-150954977	HepG2	liver:	n/a	n/a
31	E2F6	chr1:150954550-150954697	K562	blood:	n/a	n/a
32	USF2	chr1:150954289-150954811	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:150953342-150954973	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:150953545-150955004	HepG2	liver:	n/a	n/a
35	YY1	chr1:150954234-150954840	HepG2	liver:	n/a	n/a
36	ZC3H11A	chr1:150954619-150954819	K562	blood:	n/a	n/a
37	POLR2A	chr1:150954403-150954944	HepG2	liver:	n/a	n/a
38	EP300	chr1:150953590-150955177	ECC-1	luminal epithelium:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
39	TEAD4	chr1:150953538-150954765	HepG2	liver:	n/a	n/a
40	ZNF143	chr1:150954567-150954925	K562	blood:	n/a	n/a
41	CEBPB	chr1:150953482-150955441	MCF-7	breast:	n/a	chr1:150954007-150954018
42	ARID3A	chr1:150954289-150954956	HepG2	liver:	n/a	n/a
43	NFIC	chr1:150954290-150954954	HepG2	liver:	n/a	n/a
44	HNF4A	chr1:150954279-150954778	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:150954299-150954942	HepG2	liver:	n/a	n/a
46	SMC3	chr1:150954384-150954857	HepG2	liver:	n/a	n/a
47	RCOR1	chr1:150954367-150954900	HepG2	liver:	n/a	n/a
48	CUX1	chr1:150954585-150954733	K562	blood:	n/a	n/a
49	EGR1	chr1:150954607-150954936	K562	blood:	n/a	n/a
50	GATA3	chr1:150953478-150955241	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:150238576..150241529-chr1:150952972..150954986,2	MCF-7	breast:
2	chr1:150951645..150956254-chr1:150963775..150970753,11	MCF-7	breast:
3	chr1:150951870..150954741-chr1:151030040..151032027,2	K562	blood:
4	chr1:150954595..150956267-chr1:150977879..150980277,2	K562	blood:
5	chr1:150951620..150955085-chr1:150979651..150983018,4	K562	blood:
6	chr1:150532778..150534728-chr1:150954324..150956045,2	MCF-7	breast:
7	chr1:150943576..150944631-chr1:150954006..150954679,3	MCF-7	breast:
8	chr1:150953914..150954774-chr1:150980327..150981076,4	MCF-7	breast:
9	chr1:150533380..150535959-chr1:150953578..150956750,3	MCF-7	breast:
10	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:
11	chr1:150954083..150955944-chr1:151254218..151255800,2	MCF-7	breast:
12	chr1:150539071..150540911-chr1:150952638..150955044,2	MCF-7	breast:
13	chr1:150953971..150955993-chr7:99715179..99717200,2	MCF-7	breast:
14	chr1:150952337..150955570-chr1:151040233..151043325,3	MCF-7	breast:
15	chr1:149856818..149859748-chr1:150952737..150955704,2	MCF-7	breast:

No data

Variant related genes	Relation type
ANXA9	TF binding region
ENSG00000143458	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000118292	Chromatin interaction
ENSG00000117362	Chromatin interaction
ENSG00000264508	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000232671	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16841689	0.81[AFR][1000 genomes]
rs198325	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267733	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs267734	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267738	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61386199	0.95[AFR][1000 genomes]
rs73008844	0.81[AFR][1000 genomes]
rs73008850	0.81[AFR][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	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs607518	CTSK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150952000-150968000	Weak transcription	Spleen	Spleen
2	chr1:150952200-150955000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:150952600-150954800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:150952600-150957800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:150952600-150960800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:150952600-150968000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:150953200-150955400	Enhancers	Placenta	Placenta
8	chr1:150953200-150955400	Enhancers	Fetal Thymus	thymus
9	chr1:150953200-150956200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:150953200-150956200	Enhancers	Fetal Intestine Large	intestine
11	chr1:150953200-150956200	Enhancers	HMEC	breast
12	chr1:150953400-150955000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:150953400-150955000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:150953400-150955400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:150953400-150955400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:150953400-150955400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:150953600-150954800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:150953600-150954800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:150953600-150954800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:150953600-150954800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:150953600-150954800	Enhancers	Fetal Kidney	kidney
22	chr1:150953600-150954800	Enhancers	Thymus	Thymus
23	chr1:150953600-150954800	Enhancers	NHLF	lung
24	chr1:150953600-150955000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:150953600-150955000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:150953600-150955000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:150953600-150955000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:150953600-150955000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:150953600-150955000	Flanking Active TSS	A549	lung
30	chr1:150953600-150955000	Enhancers	Osteobl	bone
31	chr1:150953600-150955200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:150953600-150955200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:150953600-150955200	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr1:150953600-150955400	Enhancers	Stomach Mucosa	stomach
35	chr1:150953600-150955400	Enhancers	K562	blood
36	chr1:150953600-150955800	Enhancers	Fetal Intestine Small	intestine
37	chr1:150953600-150955800	Flanking Active TSS	HepG2	liver
38	chr1:150953600-150959000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:150953800-150954800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr1:150953800-150954800	Enhancers	HSMM	muscle
41	chr1:150953800-150955000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:150953800-150955000	Enhancers	Fetal Muscle Leg	muscle
43	chr1:150953800-150955000	Enhancers	Dnd41	blood
44	chr1:150953800-150955200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:150953800-150955200	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:150953800-150955400	Enhancers	Gastric	stomach
47	chr1:150953800-150955600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr1:150954000-150954800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:150954000-150954800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr1:150954000-150954800	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links