Variant report

Variant	rs17515715
Chromosome Location	chr2:113403306-113403307
allele	G/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	TAF1	chr2:113402747-113403992	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:113402706-113403914	K562	blood:	n/a	n/a
3	CTCF	chr2:113403160-113403310	GM12875	blood:	n/a	chr2:113403285-113403298
4	HCFC1	chr2:113401734-113404936	Hela-S3	cervix:	n/a	n/a
5	ZNF384	chr2:113403069-113403678	K562	blood:	n/a	n/a
6	POLR2A	chr2:113402569-113403760	HepG2	liver:	n/a	n/a
7	TBP	chr2:113403031-113403755	GM12878	blood:	n/a	n/a
8	CREB1	chr2:113402778-113404009	A549	lung:	n/a	n/a
9	YY1	chr2:113402638-113404290	GM12878	blood:	n/a	chr2:113403915-113403929 chr2:113403786-113403800 chr2:113403877-113403891 chr2:113403792-113403801 chr2:113403944-113403955 chr2:113403528-113403542 chr2:113404124-113404135 chr2:113403494-113403505
10	BACH1	chr2:113402870-113404599	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZEB1	chr2:113402964-113403629	GM12878	blood:	n/a	n/a
12	SIN3AK20	chr2:113402628-113404276	PANC-1	pancreas:	n/a	n/a
13	HEY1	chr2:113401600-113404264	HepG2	liver:	n/a	chr2:113403494-113403509 chr2:113403936-113403951 chr2:113403952-113403967 chr2:113403956-113403971 chr2:113403984-113403993
14	CREB1	chr2:113403202-113403699	A549	lung:	n/a	n/a
15	POLR2A	chr2:113402006-113404718	IMR90	lung:	n/a	n/a
16	NR2F2	chr2:113401604-113404921	HepG2	liver:	n/a	n/a
17	CTCF	chr2:113403075-113403329	GM10266	blood:	n/a	chr2:113403285-113403298
18	RAD21	chr2:113403110-113403365	HepG2	liver:	n/a	n/a
19	CEBPB	chr2:113403013-113403354	K562	blood:	n/a	n/a
20	MYC	chr2:113402722-113403591	K562	blood:	n/a	chr2:113403288-113403298 chr2:113403306-113403315 chr2:113403304-113403319
21	POLR2A	chr2:113402610-113404242	ECC-1	luminal epithelium:	n/a	n/a
22	JUN	chr2:113403136-113403410	H1-hESC	embryonic stem cell:	n/a	chr2:113403358-113403367
23	PAX5	chr2:113403039-113403717	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:113402635-113405101	K562	blood:	n/a	n/a
25	RAD21	chr2:113403059-113403321	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr2:113403160-113403310	GM12864	blood:	n/a	chr2:113403285-113403298
27	POLR2A	chr2:113402419-113404995	GM12891	blood:	n/a	n/a
28	RCOR1	chr2:113402708-113403805	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:113403043-113403788	SK-N-SH	brain:	n/a	n/a
30	JUND	chr2:113402824-113403845	A549	lung:	n/a	chr2:113403358-113403367 chr2:113403704-113403712
31	CTCF	chr2:113403200-113403350	HRPEpiC	eye:	n/a	chr2:113403285-113403298
32	FOSL1	chr2:113401751-113403902	HCT-116	colon:	n/a	chr2:113403358-113403367 chr2:113403704-113403712
33	NR2F2	chr2:113401628-113403847	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:113403115-113407903	K562	blood:	n/a	n/a
35	RAD21	chr2:113403034-113403378	H1-hESC	embryonic stem cell:	n/a	n/a
36	HEY1	chr2:113402617-113405042	K562	blood:	n/a	chr2:113403494-113403509 chr2:113403936-113403951 chr2:113403952-113403967 chr2:113403956-113403971 chr2:113403984-113403993
37	RFX5	chr2:113401934-113405532	Hela-S3	cervix:	n/a	chr2:113405084-113405099 chr2:113405086-113405103 chr2:113403357-113403366
38	POLR2A	chr2:113401900-113405604	HUVEC	blood vessel:	n/a	n/a
39	TCF3	chr2:113402654-113404081	GM12878	blood:	n/a	n/a
40	USF1	chr2:113402584-113403723	ECC-1	luminal epithelium:	n/a	n/a
41	TEAD4	chr2:113402946-113403686	H1-hESC	embryonic stem cell:	n/a	n/a
42	BHLHE40	chr2:113402580-113404182	GM12878	blood:	n/a	chr2:113403746-113403762
43	MAX	chr2:113402144-113404297	ECC-1	luminal epithelium:	n/a	chr2:113403983-113403993 chr2:113403984-113403993 chr2:113403983-113403994 chr2:113403984-113403994 chr2:113403288-113403298 chr2:113403306-113403315 chr2:113403985-113403992 chr2:113403304-113403319 chr2:113403984-113403993
44	RELA	chr2:113402665-113403681	GM18951	blood:	n/a	n/a
45	TAF1	chr2:113403008-113403909	GM12878	blood:	n/a	n/a
46	CTCF	chr2:113403070-113403329	H1-hESC	embryonic stem cell:	n/a	chr2:113403285-113403298
47	CBX3	chr2:113402287-113403745	K562	blood:	n/a	n/a
48	MAX	chr2:113402680-113403646	Hela-S3	cervix:	n/a	chr2:113403288-113403298 chr2:113403306-113403315 chr2:113403304-113403319
49	NFIC	chr2:113402612-113403724	HepG2	liver:	n/a	n/a
50	POLR2A	chr2:113402940-113404072	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113339547..113343883-chr2:113402286..113405078,6	K562	blood:
2	chr2:113402780..113403558-chr8:101964407..101965358,2	Hela-S3	cervix:
3	chr2:113298042..113299646-chr2:113402346..113405215,2	K562	blood:
4	chr2:112811018..112813475-chr2:113401964..113404333,2	K562	blood:
5	chr12:32552467..32553163-chr2:113403051..113404044,2	Hela-S3	cervix:
6	chr2:113403176..113405002-chr2:113522178..113523741,2	K562	blood:
7	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
8	chr2:113401688..113406035-chr2:113480430..113485744,11	MCF-7	breast:
9	chr16:81040308..81041240-chr2:113403250..113403767,2	Hela-S3	cervix:
10	chr2:113403194..113403870-chr3:169490961..169491587,2	Hela-S3	cervix:
11	chr2:113399891..113407010-chr2:113481534..113486055,14	K562	blood:
12	chr2:113031185..113034291-chr2:113402354..113405026,3	K562	blood:
13	chr10:69834544..69835281-chr2:113403250..113404083,2	Hela-S3	cervix:
14	chr2:113346825..113348931-chr2:113402265..113404788,2	MCF-7	breast:
15	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
16	chr2:113400575..113405879-chr2:113475243..113481233,15	K562	blood:
17	chr2:113400910..113403720-chr2:113487016..113489171,3	K562	blood:
18	chr2:113340437..113343949-chr2:113401268..113406617,9	MCF-7	breast:
19	chr15:64679349..64679958-chr2:113402741..113403595,2	NB4	blood:
20	chr2:113298010..113299910-chr2:113402044..113405043,2	MCF-7	breast:
21	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:
22	chr2:113345940..113348650-chr2:113401824..113404479,3	MCF-7	breast:
23	chr2:113402862..113403733-chrX:77358921..77359879,2	HCT-116	colon:
24	chr2:113297646..113299646-chr2:113402192..113403846,2	K562	blood:
25	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
26	chr2:113403244..113403947-chr4:39640189..39640861,2	Hela-S3	cervix:
27	chr2:113402977..113403864-chr8:134309881..134310413,2	Hela-S3	cervix:
28	chr2:113403189..113403992-chr3:45635124..45636083,2	Hela-S3	cervix:
29	chr17:80055916..80056452-chr2:113402977..113403764,2	Hela-S3	cervix:
30	chr2:113402414..113404382-chr2:113520815..113523652,2	MCF-7	breast:
31	chr2:113403043..113403839-chr5:137514078..137514905,2	NB4	blood:
32	chr2:113403244..113403895-chr7:1199601..1200551,2	Hela-S3	cervix:
33	chr2:113403078..113403790-chr9:3525889..3526529,2	NB4	blood:
34	chr2:113032268..113033936-chr2:113402354..113404096,2	K562	blood:
35	chr1:37939793..37940776-chr2:113402998..113403567,2	Hela-S3	cervix:
36	chr12:6862235..6862767-chr2:113403067..113404026,2	HCT-116	colon:
37	chr2:113403023..113403716-chr8:99057580..99058281,2	HCT-116	colon:
38	chr2:113339547..113342143-chr2:113401632..113406213,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CKAP2L-1	chr2:113403007-113403306	XLOC_002275
2	lnc-CKAP2L-1	chr2:113401556-113403368	NONHSAT073714

Variant related genes	Relation type
SLC20A1	TF binding region
ENSG00000237753	TF binding region
ENSG00000188177	Chromatin interaction
ENSG00000139132	Chromatin interaction
ENSG00000169607	Chromatin interaction
ENSG00000243389	Chromatin interaction
ENSG00000233621	Chromatin interaction
ENSG00000104419	Chromatin interaction
ENSG00000112983	Chromatin interaction
ENSG00000229043	Chromatin interaction
ENSG00000156482	Chromatin interaction
ENSG00000089693	Chromatin interaction
ENSG00000255458	Chromatin interaction
ENSG00000231747	Chromatin interaction
ENSG00000166803	Chromatin interaction
ENSG00000178381	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000163874	Chromatin interaction
ENSG00000169710	Chromatin interaction
ENSG00000112984	Chromatin interaction
ENSG00000148634	Chromatin interaction
ENSG00000080298	Chromatin interaction
ENSG00000228251	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000102144	Chromatin interaction
ENSG00000144791	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000085274	Chromatin interaction
ENSG00000103671	Chromatin interaction
ENSG00000163683	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10171024	0.83[EUR][1000 genomes]
rs10184339	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10758	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779885	0.82[ASN][1000 genomes]
rs11123146	0.82[ASN][1000 genomes]
rs12467747	0.82[ASN][1000 genomes]
rs12475403	0.82[ASN][1000 genomes]
rs12612089	0.82[ASN][1000 genomes]
rs17515708	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048873	0.82[ASN][1000 genomes]
rs34282612	0.89[ASN][1000 genomes]
rs35048989	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3827758	0.84[ASN][1000 genomes]
rs4261730	0.82[ASN][1000 genomes]
rs4849086	0.83[EUR][1000 genomes]
rs4849091	0.97[ASN][1000 genomes]
rs57033895	0.82[ASN][1000 genomes]
rs58662040	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58797970	0.80[ASN][1000 genomes]
rs60372418	0.83[ASN][1000 genomes]
rs6542074	0.89[ASN][1000 genomes]
rs6705487	0.83[ASN][1000 genomes]
rs6725228	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	esv3335204	chr2:113402081-113405429	Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
7	esv3329842	chr2:113402506-113405054	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113402000-113404800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:113402000-113405000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113402000-113405000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:113402200-113404400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:113402200-113404400	Active TSS	Left Ventricle	heart
6	chr2:113402200-113405200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr2:113402400-113403400	Active TSS	Aorta	Aorta
8	chr2:113402400-113404400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr2:113402400-113404400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:113402400-113404400	Active TSS	Fetal Brain Female	brain
11	chr2:113402400-113404400	Active TSS	Psoas Muscle	Psoas
12	chr2:113402400-113404800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:113402600-113403600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:113402600-113404000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:113402600-113404400	Active TSS	Brain Cingulate Gyrus	brain
16	chr2:113402600-113404400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
17	chr2:113402600-113404400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr2:113402600-113404400	Active TSS	Colon Smooth Muscle	Colon
19	chr2:113402600-113404400	Active TSS	Fetal Kidney	kidney
20	chr2:113402600-113404400	Active TSS	Lung	lung
21	chr2:113402600-113404400	Active TSS	Pancreas	Pancrea
22	chr2:113402600-113404400	Active TSS	Rectal Smooth Muscle	rectum
23	chr2:113402600-113404400	Active TSS	Right Ventricle	heart
24	chr2:113402600-113404400	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr2:113402600-113404400	Active TSS	Small Intestine	intestine
26	chr2:113402600-113404400	Active TSS	Spleen	Spleen
27	chr2:113402600-113404400	Active TSS	A549	lung
28	chr2:113402600-113404600	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr2:113402600-113404600	Active TSS	Gastric	stomach
30	chr2:113402600-113404600	Active TSS	Ovary	ovary
31	chr2:113402600-113404800	Active TSS	Esophagus	oesophagus
32	chr2:113402600-113405000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:113402600-113405200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:113402600-113405600	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr2:113402800-113403600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:113402800-113403600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:113402800-113403800	Active TSS	Thymus	Thymus
38	chr2:113402800-113404000	Active TSS	Primary B cells from peripheral blood	blood
39	chr2:113402800-113404000	Active TSS	Muscle Satellite Cultured Cells	--
40	chr2:113402800-113404000	Active TSS	Colonic Mucosa	Colon
41	chr2:113402800-113404000	Weak transcription	Fetal Brain Male	brain
42	chr2:113402800-113404000	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr2:113402800-113404200	Transcr. at gene 5' and 3'	Right Atrium	heart
44	chr2:113402800-113404200	Bivalent/Poised TSS	HepG2	liver
45	chr2:113402800-113404400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:113402800-113404400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:113402800-113404400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:113402800-113404400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:113402800-113404400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:113402800-113404400	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links