Variant report

Variant	rs4775945
Chromosome Location	chr15:51775909-51775910
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51772368..51774826-chr15:51775779..51778776,2	K562	blood:
2	chr15:51773834..51778249-chr15:51779820..51782019,4	K562	blood:

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10467923	0.80[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs11070850	0.90[EUR][1000 genomes]
rs11070852	0.97[ASN][1000 genomes]
rs11070862	0.80[CHB][hapmap]
rs11855041	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12592422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908028	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs17648128	0.82[CHB][hapmap]
rs17704742	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1869930	0.89[EUR][1000 genomes]
rs2124591	0.85[ASW][hapmap];0.95[GIH][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs2258064	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2414104	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414108	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2445746	0.86[CHB][hapmap]
rs2445751	0.86[CHB][hapmap]
rs2470192	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2470194	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2607111	0.89[EUR][1000 genomes]
rs2607113	0.87[EUR][1000 genomes]
rs28362471	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34604744	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4359386	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4436729	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4462536	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4775950	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4775967	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493498	0.95[CHB][hapmap];0.94[ASN][1000 genomes]
rs6493502	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493504	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164999	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7176988	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8024233	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8025536	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030113	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8030534	0.94[ASN][1000 genomes]
rs8034340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898135	0.86[CHB][hapmap]
rs930919	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][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	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
2	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
3	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
4	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
5	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv904218	chr15:51743186-51873407	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4775945	SCG3	cis	cerebellum	SCAN
rs4775945	SCG3	cis	parietal	SCAN
rs4775945	DMXL2	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51737000-51776400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:51738200-51784600	Weak transcription	Stomach Mucosa	stomach
3	chr15:51738400-51777400	Weak transcription	Small Intestine	intestine
4	chr15:51739000-51776000	Weak transcription	Gastric	stomach
5	chr15:51742600-51776000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:51742600-51776600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:51742600-51776800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:51743000-51780200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:51748000-51776400	Weak transcription	Right Ventricle	heart
10	chr15:51749000-51776600	Weak transcription	Fetal Kidney	kidney
11	chr15:51749200-51777400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:51750800-51776200	Weak transcription	NHDF-Ad	bronchial
13	chr15:51750800-51776600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:51750800-51777400	Weak transcription	Osteobl	bone
15	chr15:51751000-51776200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:51751000-51777400	Weak transcription	NHLF	lung
17	chr15:51751200-51777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:51751800-51776400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:51751800-51777400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:51754400-51777400	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:51763000-51776600	Weak transcription	Primary T cells from cord blood	blood
22	chr15:51763200-51776400	Weak transcription	Brain Anterior Caudate	brain
23	chr15:51763200-51777400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:51763600-51776000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:51763600-51776200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:51763600-51776400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:51763600-51826800	Weak transcription	Colonic Mucosa	Colon
28	chr15:51763800-51776000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:51763800-51776600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:51763800-51782000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:51763800-51784000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:51768800-51776000	Weak transcription	A549	lung
33	chr15:51769000-51776000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:51769000-51777200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:51773000-51776000	Weak transcription	Brain Angular Gyrus	brain
36	chr15:51773000-51782000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:51773400-51776400	Weak transcription	K562	blood
38	chr15:51773600-51776000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:51773800-51776200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:51773800-51776400	Weak transcription	Liver	Liver
41	chr15:51774000-51776600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:51774600-51779800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr15:51775000-51776600	ZNF genes & repeats	Esophagus	oesophagus
44	chr15:51775000-51776600	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr15:51775000-51776600	ZNF genes & repeats	Ovary	ovary
46	chr15:51775000-51776800	ZNF genes & repeats	Aorta	Aorta
47	chr15:51775000-51776800	ZNF genes & repeats	Lung	lung
48	chr15:51775000-51777800	ZNF genes & repeats	Brain Germinal Matrix	brain
49	chr15:51775000-51778400	ZNF genes & repeats	Adipose Nuclei	Adipose
50	chr15:51775000-51778400	ZNF genes & repeats	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links