Variant report

Variant	rs1498603
Chromosome Location	chr5:58333125-58333126
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	STAT3	chr5:58333075-58333232	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:58333046-58336833	A549	lung:	n/a	n/a
3	SIX5	chr5:58330273-58336780	A549	lung:	n/a	chr5:58334021-58334030
4	REST	chr5:58331372-58337614	A549	lung:	n/a	chr5:58334044-58334052 chr5:58335557-58335570
5	SP1	chr5:58331577-58338881	A549	lung:	n/a	chr5:58333512-58333519 chr5:58335988-58335997
6	POLR2A	chr5:58331579-58336345	IMR90	lung:	n/a	n/a
7	FOS	chr5:58333042-58333223	MCF10A-Er-Src	breast:	n/a	chr5:58333144-58333153
8	TAF1	chr5:58332948-58336675	A549	lung:	n/a	n/a
9	POLR2A	chr5:58332062-58336640	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr5:58331492-58333960	PFSK-1	brain:	n/a	n/a
11	BCL3	chr5:58330017-58334935	A549	lung:	n/a	chr5:58332249-58332258 chr5:58333393-58333401
12	POLR2A	chr5:58333105-58333313	Hela-S3	cervix:	n/a	n/a
13	EP300	chr5:58333045-58334746	A549	lung:	n/a	chr5:58333921-58333930
14	EP300	chr5:58333033-58335096	A549	lung:	n/a	chr5:58333921-58333930
15	SIN3AK20	chr5:58332967-58335742	A549	lung:	n/a	n/a
16	GATA3	chr5:58330035-58338800	A549	lung:	n/a	chr5:58333570-58333591 chr5:58332852-58332859 chr5:58333577-58333587 chr5:58333577-58333584 chr5:58332250-58332259 chr5:58333577-58333584 chr5:58332852-58332859 chr5:58333577-58333584 chr5:58333572-58333588 chr5:58336798-58336814 chr5:58332852-58332859
17	MAX	chr5:58333100-58339130	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337561-58337571 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
18	POLR2A	chr5:58331748-58336528	MCF10A-Er-Src	breast:	n/a	n/a
19	SP1	chr5:58332949-58337033	A549	lung:	n/a	chr5:58333512-58333519 chr5:58335988-58335997
20	TCF12	chr5:58331291-58337478	A549	lung:	n/a	chr5:58336418-58336428 chr5:58336399-58336408
21	CHD1	chr5:58331417-58336301	IMR90	lung:	n/a	n/a
22	MXI1	chr5:58331564-58334104	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:60729469..60730155-chr5:58333054..58333587,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247345	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10514870	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1077183	0.87[EUR][1000 genomes]
rs12657171	0.83[EUR][1000 genomes]
rs17776879	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62356693	1.00[AFR][1000 genomes]
rs71626132	0.84[AMR][1000 genomes]
rs7706419	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736186	1.00[AFR][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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58313000-58333400	Weak transcription	Lung	lung
2	chr5:58318600-58333200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58320200-58334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:58321800-58334000	Weak transcription	Gastric	stomach
5	chr5:58327000-58334000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:58329200-58333200	Enhancers	Rectal Smooth Muscle	rectum
7	chr5:58330200-58333600	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr5:58330400-58336400	Active TSS	Right Ventricle	heart
9	chr5:58330400-58336600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:58330600-58333400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:58330600-58333600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:58330600-58334600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:58330600-58335000	Transcr. at gene 5' and 3'	A549	lung
14	chr5:58330600-58336200	Active TSS	Right Atrium	heart
15	chr5:58330800-58335800	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr5:58331000-58333400	Enhancers	Fetal Heart	heart
17	chr5:58331000-58333400	Weak transcription	Small Intestine	intestine
18	chr5:58331000-58333800	Active TSS	Fetal Thymus	thymus
19	chr5:58331000-58336200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:58331000-58336400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:58331000-58336600	Active TSS	Psoas Muscle	Psoas
22	chr5:58331200-58333800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr5:58331200-58334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:58331600-58333200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:58331600-58333400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:58331600-58334200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:58331800-58333200	Weak transcription	Fetal Stomach	stomach
28	chr5:58331800-58333600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr5:58331800-58333800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:58332000-58333400	Enhancers	Hela-S3	cervix
31	chr5:58332000-58334400	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr5:58332000-58334800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr5:58332000-58335200	Active TSS	Placenta Amnion	Placenta Amnion
34	chr5:58332000-58335800	Active TSS	HSMM	muscle
35	chr5:58332200-58333200	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:58332200-58333800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:58332400-58333200	Active TSS	Stomach Smooth Muscle	stomach
38	chr5:58332400-58333400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:58332400-58333800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr5:58332400-58333800	Enhancers	NHDF-Ad	bronchial
41	chr5:58332400-58334200	Active TSS	Primary T cells fromperipheralblood	blood
42	chr5:58332400-58335000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:58332600-58333200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:58332600-58333400	Weak transcription	NH-A	brain
45	chr5:58332600-58333600	Weak transcription	HUVEC	blood vessel
46	chr5:58332600-58333800	Active TSS	HSMMtube	muscle
47	chr5:58332600-58333800	Enhancers	NHLF	lung
48	chr5:58332600-58334000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr5:58332600-58334000	Active TSS	Fetal Muscle Leg	muscle
50	chr5:58332600-58334400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links