Variant report

Variant	rs13006652
Chromosome Location	chr2:153575962-153575963
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	MBD4	chr2:153573120-153575962	HepG2	liver:	n/a	n/a
2	CUX1	chr2:153574130-153576035	K562	blood:	n/a	n/a
3	POLR2A	chr2:153572495-153576612	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr2:153575785-153576258	Hela-S3	cervix:	n/a	n/a
5	PML	chr2:153573188-153576331	K562	blood:	n/a	n/a
6	UBTF	chr2:153574751-153576003	K562	blood:	n/a	n/a
7	RELA	chr2:153573379-153576078	GM12891	blood:	n/a	n/a
8	POLR2A	chr2:153573583-153576096	GM18526	blood:	n/a	n/a
9	HEY1	chr2:153573173-153576234	K562	blood:	n/a	chr2:153575077-153575092 chr2:153575049-153575064
10	POLR2A	chr2:153573701-153576055	HCT-116	colon:	n/a	n/a
11	POLR2A	chr2:153573678-153576078	U87	brain:	n/a	n/a
12	POLR2A	chr2:153573256-153576290	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr2:153573676-153576071	H1-hESC	embryonic stem cell:	n/a	n/a
14	PRDM1	chr2:153575501-153575968	Hela-S3	cervix:	n/a	chr2:153575612-153575627
15	POLR2A	chr2:153573368-153576232	HepG2	liver:	n/a	n/a
16	YY1	chr2:153574394-153576010	ECC-1	luminal epithelium:	n/a	n/a
17	MAZ	chr2:153573347-153576076	K562	blood:	n/a	chr2:153573447-153573457
18	HEY1	chr2:153573622-153576185	K562	blood:	n/a	chr2:153575077-153575092 chr2:153575049-153575064
19	POLR2A	chr2:153573434-153576142	NB4	blood:	n/a	n/a
20	PML	chr2:153573249-153576154	GM12878	blood:	n/a	n/a
21	GTF2B	chr2:153574481-153576073	K562	blood:	n/a	n/a
22	TBP	chr2:153573346-153576089	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZNF143	chr2:153573548-153576085	GM12878	blood:	n/a	chr2:153574147-153574165 chr2:153575077-153575095
24	E2F4	chr2:153573810-153576014	MCF10A-Er-Src	breast:	n/a	chr2:153575129-153575138 chr2:153575128-153575139 chr2:153575130-153575137 chr2:153575129-153575137 chr2:153575130-153575137 chr2:153575130-153575137 chr2:153575686-153575698
25	EP300	chr2:153573778-153575983	K562	blood:	n/a	n/a
26	POLR2A	chr2:153573287-153577046	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:153572295-153576273	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr2:153573288-153576623	K562	blood:	n/a	n/a
29	POLR2A	chr2:153573591-153576232	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr2:153573348-153576064	Raji	blood:	n/a	n/a
31	MXI1	chr2:153572226-153576757	SK-N-SH	brain:	n/a	chr2:153575089-153575098
32	POLR2A	chr2:153573350-153576074	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr2:153573334-153576069	K562	blood:	n/a	n/a
34	POLR2A	chr2:153573395-153576278	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr2:153573391-153576008	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAFK	chr2:153574218-153576067	K562	blood:	n/a	n/a
37	POLR2A	chr2:153573255-153576130	GM12878	blood:	n/a	n/a
38	SIN3AK20	chr2:153573406-153576054	MCF-7	breast:	n/a	n/a
39	POLR2A	chr2:153573404-153576142	GM18505	blood:	n/a	n/a
40	POLR2A	chr2:153575749-153576228	GM12891	blood:	n/a	n/a
41	ZMIZ1	chr2:153573449-153576196	K562	blood:	n/a	n/a
42	POLR2A	chr2:153573235-153576232	GM12892	blood:	n/a	n/a
43	BCLAF1	chr2:153574989-153576334	K562	blood:	n/a	chr2:153575010-153575019
44	POLR2A	chr2:153575912-153576012	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:153572488-153577031	K562	blood:	n/a	n/a
46	IRF1	chr2:153573699-153577003	K562	blood:	n/a	chr2:153576560-153576569 chr2:153575081-153575095
47	NFIC	chr2:153573696-153575999	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:153572534-153576259	PBDE	blood:	n/a	n/a
49	POLR2A	chr2:153573494-153576086	PANC-1	pancreas:	n/a	n/a
50	FOS	chr2:153575899-153576061	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:153572649..153576015-chr2:157196773..157199686,4	K562	blood:
2	chr2:153575398..153576064-chr3:73160028..73160589,2	Hela-S3	cervix:
3	chr2:153030659..153033731-chr2:153574261..153576507,5	MCF-7	breast:
4	chr2:153575606..153576307-chr5:141392107..141392915,2	Hela-S3	cervix:
5	chr2:153575082..153576040-chr7:75676805..75677534,2	Hela-S3	cervix:

Variant related genes	Relation type
ARL6IP6	TF binding region
PRPF40A	TF binding region
ENSG00000146701	Chromatin interaction
ENSG00000127952	Chromatin interaction
ENSG00000115145	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000113552	Chromatin interaction
ENSG00000153234	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10497113	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931263	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931271	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931279	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1135617	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674911	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676069	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694512	0.84[ASN][1000 genomes]
rs11901227	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475871	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12478681	0.84[ASN][1000 genomes]
rs12693429	0.84[ASN][1000 genomes]
rs12989903	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995388	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12999331	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13003670	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13014141	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017131	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022436	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023779	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13023975	0.83[EUR][1000 genomes]
rs1370499	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831440	0.83[EUR][1000 genomes]
rs16831456	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17328776	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400456	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400938	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400952	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400980	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083097	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346551	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34199006	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34454505	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34469468	0.84[EUR][1000 genomes]
rs34619076	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775858	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35002744	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35421285	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754252	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894330	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35937874	0.92[EUR][1000 genomes]
rs36107565	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36122595	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811568	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811569	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4575677	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434172	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492085	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66849546	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728189	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736003	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417232	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417235	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72871148	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591590	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598878	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153572000-153576400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:153572000-153576400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:153572000-153576400	Active TSS	K562	blood
4	chr2:153572200-153576400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:153572200-153576400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:153572200-153576400	Active TSS	HMEC	breast
7	chr2:153572200-153576800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:153572200-153577000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:153572400-153576000	Active TSS	HSMM	muscle
10	chr2:153572400-153576200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr2:153572400-153576200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:153572400-153576400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr2:153572400-153576400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr2:153572400-153576400	Active TSS	Fetal Kidney	kidney
15	chr2:153572400-153576400	Active TSS	A549	lung
16	chr2:153572400-153576600	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr2:153572400-153576600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:153572400-153576600	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr2:153572400-153576600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:153572400-153576600	Active TSS	NHLF	lung
21	chr2:153572400-153576800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr2:153572400-153576800	Active TSS	Psoas Muscle	Psoas
23	chr2:153572400-153577000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:153572400-153577000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:153572600-153576000	Bivalent/Poised TSS	HepG2	liver
26	chr2:153572600-153576200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr2:153572600-153576200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:153572600-153576200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:153572600-153576200	Active TSS	Fetal Muscle Trunk	muscle
30	chr2:153572600-153576200	Active TSS	Right Ventricle	heart
31	chr2:153572600-153576200	Active TSS	HSMMtube	muscle
32	chr2:153572600-153576400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:153572600-153576400	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr2:153572600-153576400	Active TSS	GM12878-XiMat	blood
35	chr2:153572800-153576000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:153572800-153576000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr2:153572800-153576000	Active TSS	Fetal Intestine Large	intestine
38	chr2:153572800-153576200	Active TSS	Fetal Muscle Leg	muscle
39	chr2:153572800-153576400	Active TSS	Fetal Stomach	stomach
40	chr2:153572800-153576400	Active TSS	Fetal Thymus	thymus
41	chr2:153572800-153576400	Active TSS	Ovary	ovary
42	chr2:153572800-153576400	Active TSS	NHDF-Ad	bronchial
43	chr2:153573000-153576000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:153573000-153576000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr2:153573000-153576000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:153573000-153576000	Active TSS	Fetal Heart	heart
47	chr2:153573000-153576000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr2:153573000-153576000	Active TSS	HUVEC	blood vessel
49	chr2:153573000-153576000	Active TSS	NHEK	skin
50	chr2:153573000-153576200	Active TSS	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links