Variant report

Variant	rs12118515
Chromosome Location	chr1:45309449-45309450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45309178-45309500	HepG2	liver:	n/a	n/a
2	ZNF263	chr1:45308242-45309495	HEK293-T-REx	kidney:	n/a	chr1:45309121-45309130 chr1:45309118-45309127 chr1:45308771-45308780
3	MXI1	chr1:45308141-45309564	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45309425-45309475	GM19239	blood:	n/a
2	chr1:45309425-45309475	SAEC	small airway:	n/a
3	chr1:45309425-45309475	HCM	heart:	n/a
4	chr1:45309425-45309475	IMR90	lung:	fetal
5	chr1:45309425-45309475	HAEpiC	amniotic membrane:	n/a
6	chr1:45309425-45309475	HPAEpiC	pulmonary alveolar:	n/a
7	chr1:45309425-45309475	ProgFib	skin:	n/a
8	chr1:45309425-45309475	ECC-1	luminal epithelium:	n/a
9	chr1:45309425-45309475	AG09309	skin:	n/a
10	chr1:45309425-45309475	BJ	skin:	n/a
11	chr1:45309425-45309475	MCF-7	breast:	n/a
12	chr1:45309425-45309475	RPTEC	kidney:	n/a
13	chr1:45309425-45309475	HCT-116	colon:	n/a
14	chr1:45309425-45309475	HMEC	breast:	n/a
15	chr1:45309425-45309475	BE2_C	brain:	n/a
16	chr1:45309425-45309475	HCF	heart:	n/a
17	chr1:45309425-45309475	SK-N-MC	brain:	n/a
18	chr1:45309425-45309475	H1-hESC	embryonic stem cell:	embryo
19	chr1:45309425-45309475	MCF10A-Er-Src	breast:	n/a
20	chr1:45309425-45309475	HNPCEpiC	eye:	n/a
21	chr1:45309425-45309475	K562	blood:	n/a
22	chr1:45309425-45309475	LNCaP	prostate:	n/a
23	chr1:45309425-45309475	HEK293	kidney:	embryo
24	chr1:45309425-45309475	AG10803	skin:	n/a
25	chr1:45309425-45309475	HIPEpiC	eye:	n/a
26	chr1:45309425-45309475	NHBE	bronchial:	n/a
27	chr1:45309425-45309475	HepG2	liver:	n/a
28	chr1:45309425-45309475	AoSMC	blood vessel:	n/a
29	chr1:45309425-45309475	HCPEpiC	choroid plexus:	n/a
30	chr1:45309425-45309475	AG04450	lung:	fetal
31	chr1:45309425-45309475	AG04449	skin:	fetal
32	chr1:45309425-45309475	PANC-1	pancreas:	n/a
33	chr1:45309425-45309475	HEEpiC	esophagus:	n/a
34	chr1:45309425-45309475	GM06990	blood:	n/a
35	chr1:45309425-45309475	HRE	kidney:	n/a
36	chr1:45309425-45309475	NB4	blood:	n/a
37	chr1:45309425-45309475	CMK	blood:	n/a
38	chr1:45309425-45309475	HUVEC	blood vessel:	n/a
39	chr1:45309425-45309475	PrEC	prostate:	n/a
40	chr1:45309425-45309475	A549	lung:	n/a
41	chr1:45309425-45309475	Jurkat	blood:	n/a
42	chr1:45309425-45309475	HL-60	blood:	n/a
43	chr1:45309425-45309475	PFSK-1	brain:	n/a
44	chr1:45309425-45309475	SK-N-SH	brain:	n/a
45	chr1:45309425-45309475	ovcar-3	ovarian:	n/a
46	chr1:45309425-45309475	NT2-D1	testis:	n/a
47	chr1:45309425-45309475	NH-A	brain:	n/a
48	chr1:45309425-45309475	Hepatocyte	liver:	n/a
49	chr1:45309425-45309475	HRCEpiC	kidney:	n/a
50	chr1:45309425-45309475	T-47D	breast:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45306981..45310503-chr1:45474976..45481200,7	K562	blood:
2	chr1:45224240..45226290-chr1:45308445..45310205,2	K562	blood:
3	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
4	chr1:45307699..45310286-chr1:45986112..45988725,2	K562	blood:
5	chr1:45185746..45188870-chr1:45307191..45310438,4	K562	blood:

No data

Variant related genes	Relation type
PTCH2	TF binding region
PTCH2	CpG island
ENSG00000142945	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10158188	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211044	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211046	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211047	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11573543	0.90[ASN][1000 genomes]
rs11584031	0.80[EUR][1000 genomes]
rs12059964	0.80[ASN][1000 genomes]
rs12094007	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120470	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273940	0.92[EUR][1000 genomes]
rs263956	0.87[ASN][1000 genomes]
rs263962	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs263965	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs263975	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263977	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3795720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688465	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696675	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698951	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514741	0.90[EUR][1000 genomes]
rs7525308	0.92[EUR][1000 genomes]
rs7526786	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545808	0.92[EUR][1000 genomes]
rs7554177	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs932691	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9645347	0.92[EUR][1000 genomes]
rs9988451	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
9	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv945913	chr1:45308885-45310435	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45308200-45309600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45308400-45309600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:45308400-45309600	Enhancers	Fetal Heart	heart
4	chr1:45308600-45309600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:45308600-45309600	Enhancers	Fetal Brain Male	brain
6	chr1:45308600-45309600	Active TSS	Fetal Brain Female	brain
7	chr1:45308800-45309600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:45308800-45309600	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:45308800-45345400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:45309000-45309600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr1:45309000-45315800	Weak transcription	Lung	lung
12	chr1:45309000-45324600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:45309000-45332600	Weak transcription	Spleen	Spleen
14	chr1:45309000-45335600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:45309200-45309600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:45309200-45309600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:45309200-45313400	Weak transcription	HepG2	liver
18	chr1:45309200-45313600	Weak transcription	Primary T cells from cord blood	blood
19	chr1:45309200-45313600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:45309200-45314000	Weak transcription	Right Ventricle	heart
21	chr1:45309200-45314200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:45309200-45314400	Weak transcription	Aorta	Aorta
23	chr1:45309200-45314800	Weak transcription	Left Ventricle	heart
24	chr1:45309200-45316000	Weak transcription	Pancreas	Pancrea
25	chr1:45309200-45316200	Weak transcription	Gastric	stomach
26	chr1:45309200-45323200	Weak transcription	HSMM	muscle
27	chr1:45309200-45336800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:45309200-45337800	Weak transcription	Psoas Muscle	Psoas
29	chr1:45309200-45343000	Weak transcription	Esophagus	oesophagus
30	chr1:45309200-45345200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:45309200-45360600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:45309400-45309600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:45309400-45309600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:45309400-45309600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:45309400-45309600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:45309400-45309600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:45309400-45309600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:45309400-45309600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:45309400-45309600	Enhancers	Fetal Intestine Small	intestine
40	chr1:45309400-45309600	Enhancers	Fetal Muscle Trunk	muscle
41	chr1:45309400-45309600	Enhancers	Ovary	ovary
42	chr1:45309400-45309800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:45309400-45309800	Enhancers	Fetal Muscle Leg	muscle
44	chr1:45309400-45310000	Enhancers	Fetal Lung	lung
45	chr1:45309400-45310000	Enhancers	Fetal Stomach	stomach
46	chr1:45309400-45313400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:45309400-45313400	Weak transcription	Brain Germinal Matrix	brain
48	chr1:45309400-45313400	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:45309400-45313600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:45309400-45313600	Weak transcription	Brain Anterior Caudate	brain

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