Variant report

Variant	rs1609798
Chromosome Location	chr4:103537442-103537443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103535890..103538642-chr4:103992991..103995247,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11722146	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs11723120	0.83[CHB][hapmap]
rs12509517	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs12648696	0.94[CHB][hapmap]
rs1598859	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs1801	0.82[CHB][hapmap]
rs230498	0.80[GIH][hapmap]
rs230514	0.81[CHB][hapmap]
rs230525	0.80[CEU][hapmap]
rs230535	0.80[CEU][hapmap]
rs230539	0.82[CHB][hapmap]
rs230540	0.82[CHB][hapmap]
rs230542	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap]
rs3755867	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs3774959	0.82[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap]
rs3774963	0.82[CHB][hapmap]
rs4648055	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs4648068	0.82[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs4648133	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs4698861	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs4698863	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs9790601	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003618	chr4:103530465-103562161	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1609798	MANBA	cis	multi-tissue	Pritchard
rs1609798	ADH6	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103483400-103541600	Weak transcription	K562	blood
2	chr4:103513000-103542000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:103514600-103538200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:103514600-103539000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:103515000-103539000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:103515200-103538800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr4:103515400-103538800	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:103515400-103538800	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:103515800-103538200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:103515800-103538800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr4:103515800-103538800	Strong transcription	Rectal Smooth Muscle	rectum
12	chr4:103517600-103541600	Weak transcription	Right Atrium	heart
13	chr4:103520800-103538600	Strong transcription	GM12878-XiMat	blood
14	chr4:103521000-103538800	Strong transcription	Placenta	Placenta
15	chr4:103521200-103537600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:103521400-103554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:103523200-103538800	Strong transcription	Liver	Liver
18	chr4:103524600-103538800	Strong transcription	Dnd41	blood
19	chr4:103525800-103538800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:103527400-103538200	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:103527400-103538800	Strong transcription	Stomach Smooth Muscle	stomach
22	chr4:103527600-103538000	Strong transcription	Spleen	Spleen
23	chr4:103527600-103538200	Strong transcription	Fetal Intestine Small	intestine
24	chr4:103527600-103538800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:103527600-103538800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:103527600-103538800	Strong transcription	Fetal Intestine Large	intestine
27	chr4:103528400-103538800	Strong transcription	Pancreas	Pancrea
28	chr4:103529000-103539000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:103529600-103538800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:103529600-103538800	Strong transcription	Brain Anterior Caudate	brain
31	chr4:103529600-103538800	Strong transcription	Osteobl	bone
32	chr4:103529800-103538800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:103529800-103538800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:103529800-103539200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:103530000-103537800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:103531000-103538200	Strong transcription	Gastric	stomach
37	chr4:103531000-103538600	Strong transcription	NH-A	brain
38	chr4:103531400-103538200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:103531600-103538000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:103531600-103538200	Strong transcription	Aorta	Aorta
41	chr4:103531600-103538200	Strong transcription	Brain Substantia Nigra	brain
42	chr4:103531800-103538800	Strong transcription	Right Ventricle	heart
43	chr4:103533000-103541000	Weak transcription	Stomach Mucosa	stomach
44	chr4:103533400-103541800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:103534000-103538000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr4:103534000-103538200	Strong transcription	Fetal Lung	lung
47	chr4:103534000-103539000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr4:103534000-103540800	Weak transcription	NHDF-Ad	bronchial
49	chr4:103534000-103546200	Weak transcription	Small Intestine	intestine
50	chr4:103534400-103537800	Genic enhancers	HUVEC	blood vessel

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