Variant report

Variant	rs17051762
Chromosome Location	chr3:51389976-51389977
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10212250	0.86[JPT][hapmap]
rs1031925	0.91[CEU][hapmap];0.83[CHD][hapmap]
rs11130282	1.00[JPT][hapmap]
rs1383251	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1383252	0.84[JPT][hapmap]
rs1480353	0.91[CEU][hapmap]
rs1480357	0.86[JPT][hapmap]
rs1480358	0.86[JPT][hapmap]
rs1480363	0.86[JPT][hapmap]
rs1542574	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1552072	0.86[JPT][hapmap]
rs1552073	0.86[JPT][hapmap]
rs1552074	0.84[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17051734	0.85[JPT][hapmap]
rs2061951	0.86[JPT][hapmap]
rs2127655	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2219890	0.91[CEU][hapmap]
rs2355934	0.86[JPT][hapmap]
rs2355941	0.86[JPT][hapmap]
rs4244697	0.86[JPT][hapmap]
rs4301044	0.86[JPT][hapmap]
rs4367101	0.86[JPT][hapmap]
rs4378999	0.86[JPT][hapmap]
rs4453876	0.86[JPT][hapmap]
rs4528983	0.85[JPT][hapmap]
rs4568177	0.86[JPT][hapmap]
rs4974095	0.86[JPT][hapmap]
rs4974104	0.91[CEU][hapmap]
rs4974105	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs4974109	0.86[JPT][hapmap]
rs6445455	0.86[JPT][hapmap]
rs6445551	0.86[JPT][hapmap]
rs6445620	0.91[CEU][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs6445622	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6445628	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6772664	0.86[JPT][hapmap]
rs6777719	0.86[JPT][hapmap]
rs6779658	0.86[JPT][hapmap]
rs6809080	0.86[JPT][hapmap]
rs751075	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7619584	0.86[JPT][hapmap]
rs7625006	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7628533	0.86[JPT][hapmap]
rs7644957	0.86[JPT][hapmap]
rs7648012	0.84[CEU][hapmap]
rs922612	0.86[JPT][hapmap]
rs9855442	0.86[JPT][hapmap]
rs9858412	0.86[JPT][hapmap]
rs9878100	0.86[JPT][hapmap]
rs9883739	0.86[JPT][hapmap]

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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17051762	NCKIPSD	cis	cerebellum	SCAN
rs17051762	TEX264	cis	Nerve Tibial	GTEx
rs17051762	MST1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
2	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
6	chr3:51379000-51390200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:51379000-51393800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
9	chr3:51379200-51393600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:51379200-51393800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:51379200-51399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:51379400-51403400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:51380000-51398400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:51380000-51398400	Weak transcription	Aorta	Aorta
15	chr3:51381400-51392000	Weak transcription	Brain Anterior Caudate	brain
16	chr3:51381800-51392200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:51382800-51392200	Weak transcription	HSMMtube	muscle
18	chr3:51383000-51391000	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:51384200-51392400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:51384200-51393800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
22	chr3:51385400-51405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:51386400-51405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:51386600-51392200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:51387200-51392400	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr3:51388000-51392400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:51388000-51393600	Weak transcription	Fetal Stomach	stomach
28	chr3:51388400-51400800	Strong transcription	Brain Angular Gyrus	brain
29	chr3:51388800-51390200	Weak transcription	Fetal Brain Female	brain
30	chr3:51389000-51391800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:51389000-51392600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:51389800-51390400	Strong transcription	Brain Cingulate Gyrus	brain
33	chr3:51389800-51390600	Strong transcription	Brain Substantia Nigra	brain

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