Variant report

Variant	rs73502304
Chromosome Location	chr13:52737138-52737139
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	FOXA1	chr13:52736585-52737282	HepG2	liver:	n/a	n/a
2	EP300	chr13:52736575-52737207	HepG2	liver:	n/a	chr13:52736789-52736798
3	FOSL2	chr13:52736475-52737178	HepG2	liver:	n/a	chr13:52736788-52736798 chr13:52736789-52736798 chr13:52736788-52736797 chr13:52736787-52736799 chr13:52736789-52736796
4	POLR2A	chr13:52737115-52737270	K562	blood:	n/a	n/a
5	GATA2	chr13:52736017-52737731	HUVEC	blood vessel:	n/a	chr13:52737417-52737426 chr13:52737062-52737079 chr13:52737081-52737088 chr13:52736930-52736944
6	RCOR1	chr13:52736945-52737145	K562	blood:	n/a	n/a
7	MYC	chr13:52736932-52737169	HepG2	liver:	n/a	n/a
8	TAL1	chr13:52736866-52737147	K562	blood:	n/a	n/a
9	SP1	chr13:52736463-52737249	HepG2	liver:	n/a	chr13:52736563-52736577
10	GATA2	chr13:52736743-52737208	K562	blood:	n/a	chr13:52737062-52737079 chr13:52737081-52737088 chr13:52736930-52736944
11	MBD4	chr13:52736269-52737290	HepG2	liver:	n/a	n/a
12	POLR2A	chr13:52736839-52737143	K562	blood:	n/a	n/a
13	HDAC2	chr13:52736547-52737225	HepG2	liver:	n/a	n/a
14	MYBL2	chr13:52736426-52737291	HepG2	liver:	n/a	n/a
15	GATA3	chr13:52736526-52737143	SK-N-SH	brain:	n/a	chr13:52737062-52737079 chr13:52737081-52737088
16	RCOR1	chr13:52736870-52737142	K562	blood:	n/a	n/a
17	JUND	chr13:52736611-52737139	HepG2	liver:	n/a	chr13:52736788-52736798 chr13:52736789-52736798 chr13:52736788-52736797 chr13:52736787-52736799 chr13:52736789-52736796 chr13:52736787-52736798
18	FOXA1	chr13:52736609-52737290	HepG2	liver:	n/a	n/a
19	TEAD4	chr13:52736321-52737436	HepG2	liver:	n/a	n/a
20	NR2F2	chr13:52736584-52737269	K562	blood:	n/a	n/a
21	FOSL2	chr13:52736499-52737190	HepG2	liver:	n/a	chr13:52736788-52736798 chr13:52736789-52736798 chr13:52736788-52736797 chr13:52736787-52736799 chr13:52736789-52736796
22	EP300	chr13:52736466-52737310	HepG2	liver:	n/a	chr13:52736789-52736798
23	ARID3A	chr13:52736213-52737289	HepG2	liver:	n/a	n/a
24	NR2F2	chr13:52736323-52737168	HepG2	liver:	n/a	n/a
25	MYBL2	chr13:52736414-52737230	HepG2	liver:	n/a	n/a
26	CEBPD	chr13:52736760-52737158	K562	blood:	n/a	n/a
27	FOXA2	chr13:52736551-52737212	HepG2	liver:	n/a	n/a
28	NFIC	chr13:52736516-52737303	HepG2	liver:	n/a	n/a
29	FOXA2	chr13:52736574-52737417	HepG2	liver:	n/a	n/a
30	RXRA	chr13:52736747-52737140	HepG2	liver:	n/a	chr13:52736826-52736839 chr13:52736822-52736842 chr13:52736826-52736839 chr13:52736826-52736839
31	FOXA1	chr13:52736617-52737177	HepG2	liver:	n/a	n/a
32	NR2F2	chr13:52736506-52737428	HepG2	liver:	n/a	n/a
33	TEAD4	chr13:52736726-52737245	K562	blood:	n/a	n/a
34	NR2F2	chr13:52736704-52737269	K562	blood:	n/a	n/a
35	FOXA1	chr13:52736723-52737255	HepG2	liver:	n/a	n/a
36	EP300	chr13:52736749-52737155	HepG2	liver:	n/a	chr13:52736789-52736798
37	TCF7L2	chr13:52736193-52737342	HepG2	liver:	n/a	chr13:52736788-52736797 chr13:52736789-52736798

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52733390..52734978-chr13:52735915..52738886,2	K562	blood:

Variant related genes	Relation type
NEK3	TF binding region
ENSG00000136098	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1000892	0.92[AMR][1000 genomes]
rs17404248	0.92[AMR][1000 genomes]
rs17482550	0.92[AMR][1000 genomes]
rs17482660	0.92[AMR][1000 genomes]
rs17536694	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1886540	0.92[AMR][1000 genomes]
rs1886541	0.92[AMR][1000 genomes]
rs34288155	0.81[AMR][1000 genomes]
rs35370885	0.81[AMR][1000 genomes]
rs4480685	1.00[EUR][1000 genomes]
rs4943065	0.92[AMR][1000 genomes]
rs55969405	0.92[AMR][1000 genomes]
rs57604069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59763550	0.92[AMR][1000 genomes]
rs59924615	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61247071	0.89[AMR][1000 genomes]
rs7317742	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7320155	0.81[AMR][1000 genomes]
rs7325357	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7332381	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73500202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73502323	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7400215	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7999934	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52733800-52743000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:52733800-52757000	Weak transcription	Spleen	Spleen
3	chr13:52734000-52737400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr13:52734000-52738000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:52734000-52740200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr13:52734000-52760000	Weak transcription	Gastric	stomach
7	chr13:52734200-52737400	Enhancers	Primary hematopoietic stem cells	blood
8	chr13:52734200-52737600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr13:52734200-52737800	Enhancers	Fetal Intestine Large	intestine
10	chr13:52734200-52738000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr13:52734200-52738000	Enhancers	Fetal Intestine Small	intestine
12	chr13:52734200-52739000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr13:52734200-52739600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:52734200-52739800	Enhancers	Brain Hippocampus Middle	brain
15	chr13:52734200-52740200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr13:52734200-52741200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr13:52734200-52742200	Weak transcription	Fetal Lung	lung
18	chr13:52734200-52742400	Weak transcription	Brain Germinal Matrix	brain
19	chr13:52734200-52742400	Weak transcription	Fetal Brain Female	brain
20	chr13:52734200-52742600	Weak transcription	Esophagus	oesophagus
21	chr13:52734200-52743000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr13:52734200-52747800	Weak transcription	Fetal Brain Male	brain
23	chr13:52734200-52751800	Weak transcription	Psoas Muscle	Psoas
24	chr13:52734200-52752400	Weak transcription	GM12878-XiMat	blood
25	chr13:52734200-52754000	Weak transcription	Right Ventricle	heart
26	chr13:52734200-52754000	Weak transcription	Hela-S3	cervix
27	chr13:52734400-52737200	Enhancers	Brain Substantia Nigra	brain
28	chr13:52734400-52737400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr13:52734400-52737400	Weak transcription	Placenta	Placenta
30	chr13:52734400-52737800	Enhancers	Duodenum Mucosa	Duodenum
31	chr13:52734400-52738800	Weak transcription	Liver	Liver
32	chr13:52734400-52739200	Weak transcription	Stomach Mucosa	stomach
33	chr13:52734400-52739600	Weak transcription	Fetal Muscle Leg	muscle
34	chr13:52734400-52739600	Weak transcription	Fetal Stomach	stomach
35	chr13:52734400-52739600	Weak transcription	Ovary	ovary
36	chr13:52734400-52739600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr13:52734400-52739800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr13:52734400-52740200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr13:52734400-52741200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr13:52734400-52741600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr13:52734400-52741800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:52734400-52742400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr13:52734400-52742400	Weak transcription	Pancreas	Pancrea
44	chr13:52734400-52746000	Weak transcription	Primary B cells from cord blood	blood
45	chr13:52734400-52746200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr13:52734400-52751200	Weak transcription	Colon Smooth Muscle	Colon
47	chr13:52734400-52753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:52734400-52753600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr13:52734400-52754000	Weak transcription	NHEK	skin
50	chr13:52734400-52761000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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