Variant report

Variant	rs73489861
Chromosome Location	chr13:50511364-50511365
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	MXI1	chr13:50509251-50511503	SK-N-SH	brain:	n/a	n/a
2	ELF1	chr13:50509822-50511477	GM12878	blood:	n/a	chr13:50510642-50510651
3	MAX	chr13:50509829-50511410	ECC-1	luminal epithelium:	n/a	chr13:50511019-50511028 chr13:50511016-50511027 chr13:50510651-50510661
4	CTCF	chr13:50509622-50511370	SK-N-SH	brain:	n/a	n/a
5	SIN3A	chr13:50509764-50511413	H1-hESC	embryonic stem cell:	n/a	chr13:50510961-50510974 chr13:50511018-50511027
6	POLR2A	chr13:50509798-50511393	ECC-1	luminal epithelium:	n/a	n/a
7	EBF1	chr13:50510436-50511440	GM12878	blood:	n/a	chr13:50511294-50511307
8	MAX	chr13:50509873-50511372	ECC-1	luminal epithelium:	n/a	chr13:50511019-50511028 chr13:50511016-50511027 chr13:50510651-50510661
9	TCF12	chr13:50509960-50511391	ECC-1	luminal epithelium:	n/a	n/a
10	SIN3AK20	chr13:50509590-50511521	MCF-7	breast:	n/a	n/a
11	TEAD4	chr13:50511124-50511378	H1-hESC	embryonic stem cell:	n/a	chr13:50511251-50511260
12	ZEB1	chr13:50510319-50511386	GM12878	blood:	n/a	chr13:50510758-50510765 chr13:50510755-50510766
13	MTA3	chr13:50509601-50511512	GM12878	blood:	n/a	n/a
14	REST	chr13:50509700-50511462	H1-neurons	neurons:	n/a	chr13:50510954-50510974 chr13:50510961-50510974 chr13:50510954-50510974 chr13:50510958-50510971 chr13:50510960-50510969 chr13:50510954-50510974 chr13:50510958-50510971
15	POLR2A	chr13:50511343-50511551	Gliobla	brain:	n/a	n/a
16	MXI1	chr13:50509426-50511520	IMR90	lung:	n/a	n/a
17	POLR2A	chr13:50509778-50511451	GM12878	blood:	n/a	n/a
18	NRF1	chr13:50509306-50511444	SK-N-SH	brain:	n/a	chr13:50510639-50510648 chr13:50510696-50510710 chr13:50510693-50510707 chr13:50510696-50510707 chr13:50510696-50510707 chr13:50510698-50510707

No.	Distal block	Cell Line	Cell type
1	chr13:50509813..50511946-chr17:39844014..39846019,2	MCF-7	breast:
2	chr13:50365136..50367359-chr13:50509492..50511604,3	MCF-7	breast:
3	chr13:50510078..50512694-chr13:50569483..50571768,3	MCF-7	breast:
4	chr13:50510515..50512106-chr13:51482735..51485474,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM13-7	chr13:50510782-50513292	NONHSAT033768

Variant related genes	Relation type
SPRYD7	TF binding region
ENSG00000173812	Chromatin interaction
ENSG00000233672	Chromatin interaction
ENSG00000136104	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11617754	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2066571	0.82[ASN][1000 genomes]
rs2472599	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2475837	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28798976	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3116591	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4942899	0.82[ASN][1000 genomes]
rs7338055	0.82[ASN][1000 genomes]
rs73489862	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790943	0.83[ASN][1000 genomes]
rs7986337	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535407	0.88[ASN][1000 genomes]
rs9568354	0.87[ASN][1000 genomes]
rs9568357	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568363	0.81[ASN][1000 genomes]
rs9568364	0.81[ASN][1000 genomes]
rs9568366	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1836423	chr13:50509784-50514706	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1836704	chr13:50509784-50514706	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1838605	chr13:50509784-50514706	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1834429	chr13:50509784-50536186	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr13:50508800-50511400	Active TSS	Right Atrium	heart
2	chr13:50509000-50511400	Active TSS	A549	lung
3	chr13:50509000-50511400	Active TSS	K562	blood
4	chr13:50509000-50511600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:50509000-50511600	Active TSS	HMEC	breast
6	chr13:50509000-50511800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:50509200-50511400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:50509400-50511400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr13:50509400-50511400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr13:50509400-50511400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr13:50509400-50511400	Active TSS	Fetal Intestine Large	intestine
12	chr13:50509400-50511400	Active TSS	HSMMtube	muscle
13	chr13:50509400-50511600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:50509400-50511600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr13:50509400-50511600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:50509400-50511600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:50509400-50511600	Active TSS	NHLF	lung
18	chr13:50509600-50511400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr13:50509600-50511400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:50509600-50511400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:50509600-50511400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:50509600-50511400	Active TSS	Aorta	Aorta
23	chr13:50509600-50511400	Active TSS	Brain Cingulate Gyrus	brain
24	chr13:50509600-50511400	Active TSS	Esophagus	oesophagus
25	chr13:50509600-50511400	Active TSS	Left Ventricle	heart
26	chr13:50509600-50511400	Active TSS	Ovary	ovary
27	chr13:50509600-50511400	Active TSS	Pancreas	Pancrea
28	chr13:50509600-50511400	Active TSS	Placenta Amnion	Placenta Amnion
29	chr13:50509600-50511400	Active TSS	HepG2	liver
30	chr13:50509600-50511400	Active TSS	HSMM	muscle
31	chr13:50509600-50511400	Active TSS	NHDF-Ad	bronchial
32	chr13:50509600-50511600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:50509600-50511600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr13:50509600-50511600	Active TSS	Fetal Kidney	kidney
35	chr13:50509600-50511800	Active TSS	Colonic Mucosa	Colon
36	chr13:50509600-50511800	Active TSS	NHEK	skin
37	chr13:50509800-50511400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr13:50509800-50511400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr13:50509800-50511400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:50509800-50511400	Active TSS	Brain Substantia Nigra	brain
41	chr13:50509800-50511400	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr13:50509800-50511400	Active TSS	Small Intestine	intestine
43	chr13:50509800-50511600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:50509800-50511600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:50509800-50511600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:50509800-50511600	Active TSS	Brain Angular Gyrus	brain
47	chr13:50509800-50511600	Active TSS	Colon Smooth Muscle	Colon
48	chr13:50509800-50511600	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr13:50509800-50511600	Active TSS	Fetal Brain Female	brain
50	chr13:50509800-50511600	Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links