Variant report

Variant	rs73489862
Chromosome Location	chr13:50511421-50511422
allele	A/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	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	EBF1	chr13:50510436-50511440	GM12878	blood:	n/a	chr13:50511294-50511307
4	SIN3AK20	chr13:50509590-50511521	MCF-7	breast:	n/a	n/a
5	MTA3	chr13:50509601-50511512	GM12878	blood:	n/a	n/a
6	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
7	POLR2A	chr13:50511343-50511551	Gliobla	brain:	n/a	n/a
8	MXI1	chr13:50509426-50511520	IMR90	lung:	n/a	n/a
9	POLR2A	chr13:50509778-50511451	GM12878	blood:	n/a	n/a
10	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
ENSG00000136104	Chromatin interaction
ENSG00000233672	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000102753	Chromatin interaction
ENSG00000264864	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	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2066571	0.82[ASN][1000 genomes]
rs2472599	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2475837	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28798976	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3116591	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4942899	0.82[ASN][1000 genomes]
rs7338055	0.82[ASN][1000 genomes]
rs73489861	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	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535407	0.88[ASN][1000 genomes]
rs9568354	0.87[ASN][1000 genomes]
rs9568357	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50509000-50511600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:50509000-50511600	Active TSS	HMEC	breast
3	chr13:50509000-50511800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:50509400-50511600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr13:50509400-50511600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr13:50509400-50511600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:50509400-50511600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:50509400-50511600	Active TSS	NHLF	lung
9	chr13:50509600-50511600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:50509600-50511600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr13:50509600-50511600	Active TSS	Fetal Kidney	kidney
12	chr13:50509600-50511800	Active TSS	Colonic Mucosa	Colon
13	chr13:50509600-50511800	Active TSS	NHEK	skin
14	chr13:50509800-50511600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:50509800-50511600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:50509800-50511600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:50509800-50511600	Active TSS	Brain Angular Gyrus	brain
18	chr13:50509800-50511600	Active TSS	Colon Smooth Muscle	Colon
19	chr13:50509800-50511600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr13:50509800-50511600	Active TSS	Fetal Brain Female	brain
21	chr13:50509800-50511600	Active TSS	Right Ventricle	heart
22	chr13:50509800-50511600	Active TSS	Osteobl	bone
23	chr13:50509800-50511800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr13:50509800-50511800	Active TSS	Rectal Smooth Muscle	rectum
25	chr13:50509800-50512000	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr13:50510000-50511600	Active TSS	Primary T cells from cord blood	blood
27	chr13:50510000-50512000	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr13:50510400-50512000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:50510800-50511600	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr13:50510800-50511600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr13:50510800-50511600	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr13:50510800-50511600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr13:50510800-50511600	Flanking Active TSS	Dnd41	blood
34	chr13:50510800-50511800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr13:50510800-50511800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:50510800-50511800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr13:50511000-50511600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr13:50511000-50511600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr13:50511000-50511600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr13:50511000-50511600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr13:50511000-50511600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr13:50511000-50511600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr13:50511000-50511600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr13:50511000-50511600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:50511000-50511600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr13:50511000-50511600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr13:50511200-50511600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr13:50511200-50511600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr13:50511200-50511600	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr13:50511200-50511600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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