Variant report

Variant	rs57560404
Chromosome Location	chr13:80055907-80055908
allele	C/G
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	POLR2A	chr13:80054945-80056239	GM19193	blood:	n/a	n/a
2	MAX	chr13:80055138-80056073	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr13:80054932-80056167	GM12892	blood:	n/a	n/a
4	NFIC	chr13:80055744-80056123	GM12878	blood:	n/a	n/a
5	POLR2A	chr13:80054410-80058154	MCF10A-Er-Src	breast:	n/a	n/a
6	CHD2	chr13:80055026-80056145	Hela-S3	cervix:	n/a	chr13:80055227-80055234
7	ZEB1	chr13:80054925-80056201	GM12878	blood:	n/a	chr13:80055818-80055825
8	UBTF	chr13:80055170-80056171	K562	blood:	n/a	n/a
9	TEAD4	chr13:80055903-80056272	K562	blood:	n/a	n/a
10	BACH1	chr13:80055001-80056103	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr13:80054931-80055936	GM19099	blood:	n/a	n/a
12	STAT3	chr13:80055842-80056697	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr13:80055007-80056136	HepG2	liver:	n/a	n/a
14	POLR2A	chr13:80055015-80056273	Hela-S3	cervix:	n/a	n/a
15	BRCA1	chr13:80055798-80055921	GM12878	blood:	n/a	n/a
16	STAT3	chr13:80055844-80056287	MCF10A-Er-Src	breast:	n/a	n/a
17	ARID3A	chr13:80055729-80055976	HepG2	liver:	n/a	n/a
18	PML	chr13:80055071-80056263	GM12878	blood:	n/a	n/a
19	NRF1	chr13:80054874-80055928	SK-N-SH	brain:	n/a	chr13:80055360-80055371 chr13:80055221-80055230
20	SMARCB1	chr13:80054933-80056232	Hela-S3	cervix:	n/a	n/a
21	STAT5A	chr13:80055295-80056291	GM12878	blood:	n/a	n/a
22	POLR2A	chr13:80054892-80055932	MCF-7	breast:	n/a	n/a
23	POLR2A	chr13:80054859-80056291	PBDE	blood:	n/a	n/a
24	FOS	chr13:80055873-80056213	MCF10A-Er-Src	breast:	n/a	chr13:80055987-80055997 chr13:80055969-80055978 chr13:80055987-80055997
25	YY1	chr13:80055737-80056131	GM12878	blood:	n/a	n/a
26	ZEB1	chr13:80054923-80056238	HepG2	liver:	n/a	chr13:80055818-80055825
27	HCFC1	chr13:80054908-80056315	Hela-S3	cervix:	n/a	n/a
28	MXI1	chr13:80055235-80056073	Hela-S3	cervix:	n/a	n/a
29	TAF1	chr13:80055046-80056012	ECC-1	luminal epithelium:	n/a	n/a
30	RCOR1	chr13:80055150-80055925	K562	blood:	n/a	n/a
31	POLR2A	chr13:80055144-80056216	Hela-S3	cervix:	n/a	n/a
32	RCOR1	chr13:80055010-80055977	GM12878	blood:	n/a	n/a
33	STAT3	chr13:80055602-80056572	MCF10A-Er-Src	breast:	n/a	n/a
34	ELF1	chr13:80054990-80055932	GM12878	blood:	n/a	chr13:80055695-80055707 chr13:80055464-80055477
35	FOS	chr13:80055844-80056210	MCF10A-Er-Src	breast:	n/a	chr13:80055987-80055997 chr13:80055969-80055978 chr13:80055987-80055997
36	JUND	chr13:80055321-80055990	H1-hESC	embryonic stem cell:	n/a	chr13:80055969-80055978
37	BRCA1	chr13:80055447-80056243	Hela-S3	cervix:	n/a	n/a
38	MAZ	chr13:80055138-80056117	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr13:80054937-80056085	GM18951	blood:	n/a	n/a
40	ZNF263	chr13:80055113-80056251	HEK293-T-REx	kidney:	n/a	n/a
41	ZNF384	chr13:80055848-80056184	K562	blood:	n/a	n/a
42	MYC	chr13:80055025-80056140	MCF10A-Er-Src	breast:	n/a	n/a
43	MXI1	chr13:80054593-80056424	SK-N-SH	brain:	n/a	n/a
44	REST	chr13:80054870-80056067	H1-neurons	neurons:	n/a	chr13:80055269-80055279
45	ZC3H11A	chr13:80055074-80055973	K562	blood:	n/a	n/a
46	UBTF	chr13:80055211-80056083	K562	blood:	n/a	n/a
47	STAT3	chr13:80055804-80056277	MCF10A-Er-Src	breast:	n/a	n/a
48	MYC	chr13:80054812-80056197	NB4	blood:	n/a	n/a
49	POLR2A	chr13:80054898-80056077	HEK293	kidney:	n/a	n/a
50	POLR2A	chr13:80054937-80056085	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:80055092..80056068-chr5:162886605..162887237,2	Hela-S3	cervix:
2	chr1:117113119..117113966-chr13:80055132..80056028,2	NB4	blood:
3	chr13:79977332..79980292-chr13:80055643..80057700,2	K562	blood:
4	chr13:79980450..79981962-chr13:80054323..80056011,2	K562	blood:
5	chr13:79979196..79982246-chr13:80054691..80057070,3	MCF-7	breast:

Variant related genes	Relation type
NDFIP2-AS1	TF binding region
ENSG00000170584	Chromatin interaction
ENSG00000116815	Chromatin interaction
ENSG00000227354	Chromatin interaction
ENSG00000139746	Chromatin interaction
ENSG00000072571	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs17071373	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071564	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071576	1.00[AMR][1000 genomes]
rs17071581	1.00[AMR][1000 genomes]
rs17071592	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071596	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071599	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071601	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17071609	1.00[AMR][1000 genomes]
rs17071610	1.00[AMR][1000 genomes]
rs17071613	1.00[AMR][1000 genomes]
rs17071624	1.00[AMR][1000 genomes]
rs55887763	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56737007	1.00[AMR][1000 genomes]
rs56823234	1.00[AMR][1000 genomes]
rs57066341	1.00[AMR][1000 genomes]
rs57068944	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57603166	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57615648	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57863151	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58006070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58088304	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58260634	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58322995	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58325260	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58379158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58833188	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58930697	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59105864	1.00[AMR][1000 genomes]
rs59232955	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59245717	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59331936	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59604922	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59945183	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60119719	0.94[AFR][1000 genomes]
rs60183984	1.00[AMR][1000 genomes]
rs60240323	1.00[AMR][1000 genomes]
rs60575675	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60827595	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61216430	1.00[AMR][1000 genomes]
rs61368443	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61464969	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7139938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7323341	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7324225	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7328479	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7332059	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7332241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7337248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73548917	1.00[AMR][1000 genomes]
rs73548923	1.00[AMR][1000 genomes]
rs73548924	1.00[AMR][1000 genomes]
rs73548926	1.00[AMR][1000 genomes]
rs73548938	1.00[AMR][1000 genomes]
rs73548941	1.00[AMR][1000 genomes]
rs73548942	1.00[AMR][1000 genomes]
rs73549001	1.00[AMR][1000 genomes]
rs73551505	1.00[AMR][1000 genomes]
rs73551522	1.00[AMR][1000 genomes]
rs73551530	1.00[AMR][1000 genomes]
rs73551537	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551544	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551547	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551548	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551551	1.00[AMR][1000 genomes]
rs73551555	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551562	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551563	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551564	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551566	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551567	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551569	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551570	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551575	1.00[AMR][1000 genomes]
rs73551578	1.00[AMR][1000 genomes]
rs73551581	1.00[AMR][1000 genomes]
rs73551583	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551589	1.00[AMR][1000 genomes]
rs73551592	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551599	1.00[AMR][1000 genomes]
rs73553407	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553414	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553416	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553419	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553423	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73553442	1.00[AMR][1000 genomes]
rs73553454	1.00[AMR][1000 genomes]
rs73553459	1.00[AMR][1000 genomes]
rs73564691	1.00[AMR][1000 genomes]
rs73566444	1.00[AMR][1000 genomes]
rs74098262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74100736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7983904	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7988143	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7990488	0.91[AFR][1000 genomes];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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 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	chr13:80054600-80056400	Active TSS	Brain Angular Gyrus	brain
2	chr13:80054600-80056600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr13:80054600-80056800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr13:80054600-80056800	Active TSS	A549	lung
5	chr13:80054800-80056000	Active TSS	Brain Anterior Caudate	brain
6	chr13:80054800-80056000	Active TSS	Brain Cingulate Gyrus	brain
7	chr13:80054800-80056000	Active TSS	Brain Substantia Nigra	brain
8	chr13:80054800-80056000	Active TSS	Fetal Kidney	kidney
9	chr13:80054800-80056000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
10	chr13:80054800-80056000	Bivalent/Poised TSS	Fetal Stomach	stomach
11	chr13:80054800-80056200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr13:80054800-80056200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:80054800-80056200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr13:80054800-80056400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:80054800-80056400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr13:80054800-80056400	Active TSS	Muscle Satellite Cultured Cells	--
17	chr13:80054800-80056400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:80054800-80056400	Active TSS	Colon Smooth Muscle	Colon
19	chr13:80054800-80056400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr13:80054800-80056400	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr13:80054800-80056400	Active TSS	GM12878-XiMat	blood
22	chr13:80054800-80056600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr13:80054800-80056600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:80054800-80056600	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr13:80054800-80056600	Active TSS	Liver	Liver
26	chr13:80054800-80056600	Active TSS	Brain Hippocampus Middle	brain
27	chr13:80054800-80056600	Active TSS	Hela-S3	cervix
28	chr13:80054800-80056600	Active TSS	HSMM	muscle
29	chr13:80054800-80057000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:80054800-80057000	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr13:80054800-80057000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:80054800-80057000	Active TSS	Right Atrium	heart
33	chr13:80054800-80057000	Active TSS	K562	blood
34	chr13:80054800-80057200	Active TSS	Colonic Mucosa	Colon
35	chr13:80054800-80057200	Active TSS	Rectal Smooth Muscle	rectum
36	chr13:80054800-80057400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr13:80054800-80057600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr13:80054800-80057800	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr13:80054800-80057800	Active TSS	Fetal Intestine Large	intestine
40	chr13:80054800-80057800	Active TSS	Fetal Intestine Small	intestine
41	chr13:80054800-80058000	Active TSS	Duodenum Mucosa	Duodenum
42	chr13:80054800-80059400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr13:80055000-80056000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:80055000-80056000	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr13:80055000-80056000	Active TSS	Primary T cells from cord blood	blood
46	chr13:80055000-80056000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:80055000-80056000	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr13:80055000-80056000	Active TSS	Gastric	stomach
49	chr13:80055000-80056000	Active TSS	Left Ventricle	heart
50	chr13:80055000-80056000	Active TSS	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links