Variant report

Variant	rs4775941
Chromosome Location	chr15:51659830-51659831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51572199..51575130-chr15:51658067..51661201,3	MCF-7	breast:
2	chr15:51642370..51644642-chr15:51658744..51660938,2	MCF-7	breast:
3	chr15:51606490..51608990-chr15:51658580..51661011,2	MCF-7	breast:
4	chr15:51633614..51635996-chr15:51658332..51660020,2	MCF-7	breast:
5	chr15:51651683..51656277-chr15:51657085..51661160,7	MCF-7	breast:
6	chr15:51631962..51635284-chr15:51658030..51661576,5	MCF-7	breast:
7	chr15:51655989..51658966-chr15:51659678..51663133,3	K562	blood:

Variant related genes	Relation type
ENSG00000259306	Chromatin interaction
ENSG00000270378	Chromatin interaction
ENSG00000186417	Chromatin interaction
ENSG00000259701	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12592994	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2445782	0.86[EUR][1000 genomes]
rs2470174	0.88[GIH][hapmap]
rs28757061	1.00[YRI][hapmap]
rs28757094	1.00[ASW][hapmap]
rs28757105	1.00[ASW][hapmap]
rs28757106	1.00[ASW][hapmap]
rs28757108	1.00[ASW][hapmap]
rs28757127	1.00[ASW][hapmap]
rs28757142	1.00[ASW][hapmap]
rs28757146	1.00[ASW][hapmap]
rs28757148	1.00[YRI][hapmap]
rs4533220	1.00[ASW][hapmap]
rs4774588	0.85[CEU][hapmap]
rs57046498	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4775941	SLC30A4	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51640800-51676200	Weak transcription	Aorta	Aorta
2	chr15:51649600-51660600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:51656000-51663400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:51656400-51661200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:51656600-51661400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:51657800-51660400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:51657800-51662600	Enhancers	Placenta	Placenta
8	chr15:51657800-51662600	Enhancers	Stomach Mucosa	stomach
9	chr15:51658400-51660200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr15:51658400-51661400	Enhancers	Fetal Muscle Leg	muscle
11	chr15:51658400-51661600	Enhancers	Brain Substantia Nigra	brain
12	chr15:51658800-51660000	Enhancers	Adipose Nuclei	Adipose
13	chr15:51659000-51660000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:51659000-51660400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:51659000-51661600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:51659000-51662200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:51659200-51660000	Flanking Active TSS	A549	lung
18	chr15:51659200-51660600	Enhancers	Brain Hippocampus Middle	brain
19	chr15:51659200-51661600	Enhancers	Brain Angular Gyrus	brain
20	chr15:51659200-51661600	Enhancers	Stomach Smooth Muscle	stomach
21	chr15:51659200-51661800	Enhancers	Hela-S3	cervix
22	chr15:51659200-51661800	Enhancers	NHDF-Ad	bronchial
23	chr15:51659200-51662600	Enhancers	Osteobl	bone
24	chr15:51659400-51660000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:51659400-51660000	Enhancers	Esophagus	oesophagus
26	chr15:51659400-51660000	Flanking Active TSS	HepG2	liver
27	chr15:51659400-51660200	Enhancers	Duodenum Mucosa	Duodenum
28	chr15:51659400-51660200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:51659400-51660200	Enhancers	Left Ventricle	heart
30	chr15:51659400-51660600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:51659400-51662400	Enhancers	NHLF	lung
32	chr15:51659400-51662600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr15:51659600-51660000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr15:51659600-51660000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:51659600-51660000	Enhancers	Brain Germinal Matrix	brain
36	chr15:51659600-51660400	Enhancers	Fetal Intestine Small	intestine
37	chr15:51659600-51660600	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr15:51659800-51660000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr15:51659800-51660200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:51659800-51660200	Weak transcription	NH-A	brain
41	chr15:51659800-51661200	Enhancers	Fetal Lung	lung
42	chr15:51659800-51661200	Weak transcription	Ovary	ovary
43	chr15:51659800-51661200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr15:51659800-51661400	Enhancers	Gastric	stomach
45	chr15:51659800-51661800	Enhancers	Brain Inferior Temporal Lobe	brain

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