Variant report

Variant	rs6493395
Chromosome Location	chr15:50343984-50343985
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	CTCF	chr15:50343981-50344364	HepG2	liver:	n/a	chr15:50344208-50344229 chr15:50344213-50344231
2	POLR2A	chr15:50343982-50344100	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr15:50343804-50344595	A549	lung:	n/a	n/a
4	FOXA1	chr15:50343970-50344391	HepG2	liver:	n/a	chr15:50344097-50344112
5	CEBPB	chr15:50343972-50344371	Hela-S3	cervix:	n/a	n/a
6	RAD21	chr15:50343877-50344551	A549	lung:	n/a	chr15:50344211-50344230
7	BCL3	chr15:50343838-50344498	A549	lung:	n/a	n/a
8	FOSL2	chr15:50343898-50344405	A549	lung:	n/a	n/a
9	CEBPB	chr15:50343729-50344508	A549	lung:	n/a	n/a
10	FOS	chr15:50343948-50344330	MCF10A-Er-Src	breast:	n/a	n/a
11	MAFK	chr15:50343572-50344315	IMR90	lung:	n/a	n/a
12	CEBPB	chr15:50343938-50344364	A549	lung:	n/a	n/a
13	SMC3	chr15:50343790-50344902	SK-N-SH	brain:	n/a	chr15:50344218-50344228
14	RAD21	chr15:50343963-50344340	SK-N-SH_RA	brain:	n/a	chr15:50344211-50344230
15	RAD21	chr15:50343926-50344492	H1-hESC	embryonic stem cell:	n/a	chr15:50344211-50344230
16	CTCF	chr15:50343933-50344643	MCF-7	breast:	n/a	chr15:50344208-50344229 chr15:50344213-50344231
17	FOXA1	chr15:50343974-50344334	HepG2	liver:	n/a	chr15:50344097-50344112
18	FOXA1	chr15:50343959-50344333	HepG2	liver:	n/a	chr15:50344097-50344112
19	TCF12	chr15:50343660-50344552	A549	lung:	n/a	n/a
20	USF1	chr15:50343879-50344373	A549	lung:	n/a	n/a
21	SP1	chr15:50343795-50344465	A549	lung:	n/a	n/a
22	RAD21	chr15:50343935-50344397	SK-N-SH_RA	brain:	n/a	chr15:50344211-50344230
23	TCF12	chr15:50343884-50344370	A549	lung:	n/a	n/a
24	FOXA2	chr15:50343884-50344469	A549	lung:	n/a	n/a
25	RFX5	chr15:50343767-50344476	SK-N-SH	brain:	n/a	chr15:50343940-50343953 chr15:50344191-50344206
26	CTCF	chr15:50343976-50344534	IMR90	lung:	n/a	chr15:50344208-50344229 chr15:50344213-50344231
27	CTCF	chr15:50343894-50344527	HCT-116	colon:	n/a	chr15:50344208-50344229 chr15:50344213-50344231
28	SMC3	chr15:50343945-50344492	Hela-S3	cervix:	n/a	chr15:50344218-50344228
29	RAD21	chr15:50343928-50344441	HepG2	liver:	n/a	chr15:50344211-50344230
30	RAD21	chr15:50343979-50344448	ECC-1	luminal epithelium:	n/a	chr15:50344211-50344230
31	RAD21	chr15:50343778-50344584	A549	lung:	n/a	chr15:50344211-50344230
32	RAD21	chr15:50343423-50344658	SK-N-SH	brain:	n/a	chr15:50344211-50344230
33	ZBTB33	chr15:50343917-50344428	A549	lung:	n/a	n/a
34	RAD21	chr15:50343759-50344648	MCF-7	breast:	n/a	chr15:50344211-50344230
35	SP1	chr15:50343829-50344466	A549	lung:	n/a	n/a
36	RAD21	chr15:50343868-50344449	HCT-116	colon:	n/a	chr15:50344211-50344230
37	FOXA1	chr15:50343952-50344282	HepG2	liver:	n/a	chr15:50344097-50344112
38	RAD21	chr15:50343944-50344406	H1-hESC	embryonic stem cell:	n/a	chr15:50344211-50344230
39	CTCF	chr15:50343960-50344110	A549	lung:	n/a	n/a
40	CEBPB	chr15:50343871-50344450	MCF-7	breast:	n/a	n/a
41	STAT3	chr15:50343768-50344254	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr15:50343983-50344316	H1-hESC	embryonic stem cell:	n/a	chr15:50344208-50344229 chr15:50344213-50344231
43	RAD21	chr15:50343884-50344458	MCF-7	breast:	n/a	chr15:50344211-50344230
44	RAD21	chr15:50343902-50344651	IMR90	lung:	n/a	chr15:50344211-50344230
45	CTCF	chr15:50343903-50344437	A549	lung:	n/a	chr15:50344208-50344229 chr15:50344213-50344231
46	RAD21	chr15:50343919-50344480	ECC-1	luminal epithelium:	n/a	chr15:50344211-50344230
47	CEBPB	chr15:50343964-50344366	IMR90	lung:	n/a	n/a
48	FOS	chr15:50343960-50344331	MCF10A-Er-Src	breast:	n/a	n/a
49	MAFK	chr15:50343601-50344326	HepG2	liver:	n/a	n/a
50	RAD21	chr15:50343895-50344456	Hela-S3	cervix:	n/a	chr15:50344211-50344230

No.	Distal block	Cell Line	Cell type
1	chr15:50343838..50344709-chr15:50437300..50438173,3	MCF-7	breast:
2	chr15:50293833..50297239-chr15:50342287..50344568,3	MCF-7	breast:
3	chr15:50167729..50168355-chr15:50343722..50344667,4	MCF-7	breast:
4	chr15:50295364..50296554-chr15:50343746..50344327,4	MCF-7	breast:
5	chr15:49813709..49814641-chr15:50343905..50344674,5	MCF-7	breast:
6	chr15:50295676..50296612-chr15:50343747..50344632,9	MCF-7	breast:
7	chr15:50168577..50169691-chr15:50343449..50344653,12	MCF-7	breast:
8	chr15:50343799..50344658-chr15:50430684..50431213,3	MCF-7	breast:
9	chr15:50343772..50344353-chr15:50420107..50421113,3	MCF-7	breast:
10	chr15:50124508..50125493-chr15:50343834..50344700,3	MCF-7	breast:
11	chr15:50168669..50169329-chr15:50343948..50344644,2	MCF-7	breast:
12	chr15:49813884..49814632-chr15:50343852..50344661,2	MCF-7	breast:
13	chr15:50342963..50345133-chr15:50348674..50350890,2	MCF-7	breast:
14	chr15:50166426..50168186-chr15:50342851..50345400,2	MCF-7	breast:

Variant related genes	Relation type
ATP8B4	TF binding region
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10519258	1.00[GIH][hapmap]
rs11070744	1.00[GIH][hapmap];1.00[AFR][1000 genomes]
rs11070746	1.00[GIH][hapmap]
rs11853146	1.00[GIH][hapmap]
rs2414009	1.00[GIH][hapmap];1.00[AFR][1000 genomes]
rs3803371	0.83[GIH][hapmap]
rs4451890	1.00[AFR][1000 genomes]
rs6493398	1.00[AFR][1000 genomes]
rs6493399	0.85[GIH][hapmap];1.00[AFR][1000 genomes]
rs7163415	1.00[GIH][hapmap];1.00[AFR][1000 genomes]
rs7176967	1.00[AFR][1000 genomes]
rs72734852	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8036963	1.00[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv904207	chr15:50290295-50352945	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1530	chr15:50302524-50347616	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6493395	SLC24A5	cis	cerebellum	SCAN
rs6493395	DUOX2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50337400-50347400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:50337800-50344200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:50339400-50347200	Weak transcription	Aorta	Aorta
4	chr15:50341200-50347000	Weak transcription	Right Atrium	heart
5	chr15:50341400-50346200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:50341600-50347000	Enhancers	NHDF-Ad	bronchial
7	chr15:50341600-50347200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:50342400-50347400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:50343000-50351200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr15:50343200-50344400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:50343200-50347000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:50343200-50347000	Enhancers	Osteobl	bone
13	chr15:50343400-50346000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:50343400-50352000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr15:50343400-50352400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:50343600-50344200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:50343600-50344600	Enhancers	Brain Angular Gyrus	brain
18	chr15:50343600-50344600	Enhancers	Brain Hippocampus Middle	brain
19	chr15:50343600-50344600	Enhancers	Colon Smooth Muscle	Colon
20	chr15:50343600-50344800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:50343600-50344800	Enhancers	Rectal Smooth Muscle	rectum
22	chr15:50343600-50344800	Enhancers	Hela-S3	cervix
23	chr15:50343600-50344800	Enhancers	HSMM	muscle
24	chr15:50343600-50348600	Enhancers	Fetal Intestine Large	intestine
25	chr15:50343800-50344200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:50343800-50344200	Flanking Active TSS	A549	lung
27	chr15:50343800-50344200	Weak transcription	NHLF	lung
28	chr15:50343800-50344600	Enhancers	Brain Substantia Nigra	brain
29	chr15:50343800-50344600	Enhancers	Fetal Kidney	kidney
30	chr15:50343800-50344600	Enhancers	Fetal Lung	lung
31	chr15:50343800-50344600	Enhancers	Fetal Stomach	stomach
32	chr15:50343800-50345400	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr15:50343800-50346200	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links