Variant report

Variant	rs173369
Chromosome Location	chr3:155419109-155419110
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155406187..155408621-chr3:155417875..155419444,2	K562	blood:
2	chr3:155099375..155100930-chr3:155418818..155420546,12	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10936006	0.80[JPT][hapmap]
rs10936014	0.82[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12053896	0.81[CHB][hapmap]
rs12632699	0.90[JPT][hapmap]
rs1401695	0.90[JPT][hapmap]
rs1607590	0.90[JPT][hapmap]
rs1607591	0.91[JPT][hapmap]
rs181696	0.85[JPT][hapmap]
rs183088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878859	0.88[JPT][hapmap]
rs1879089	0.90[JPT][hapmap]
rs189639	0.91[JPT][hapmap]
rs1914799	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs193313	0.89[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2015945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2102897	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2203885	0.95[JPT][hapmap]
rs2315589	0.95[JPT][hapmap]
rs2315590	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs358705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358712	0.80[MEX][hapmap]
rs358726	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs358729	0.82[AMR][1000 genomes]
rs358908	0.82[JPT][hapmap]
rs358909	0.82[JPT][hapmap]
rs359539	0.90[JPT][hapmap]
rs359540	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs359542	0.85[JPT][hapmap]
rs359549	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs359551	0.91[JPT][hapmap]
rs359552	0.91[JPT][hapmap]
rs359553	0.90[JPT][hapmap]
rs359554	0.91[JPT][hapmap]
rs359556	0.91[JPT][hapmap]
rs359557	0.91[JPT][hapmap]
rs359561	0.90[JPT][hapmap]
rs359565	0.89[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs359566	0.90[JPT][hapmap]
rs359568	0.91[JPT][hapmap]
rs359569	0.91[JPT][hapmap]
rs359570	0.91[JPT][hapmap]
rs378905	0.80[MEX][hapmap]
rs3908138	0.90[JPT][hapmap]
rs3908140	0.91[JPT][hapmap]
rs3908141	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs3908144	0.90[JPT][hapmap]
rs3914780	0.90[JPT][hapmap]
rs392521	0.80[MEX][hapmap]
rs394419	0.80[MEX][hapmap]
rs407033	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs410115	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4125975	0.90[JPT][hapmap]
rs416494	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4287944	0.94[JPT][hapmap]
rs430008	0.80[MEX][hapmap]
rs4401403	0.90[JPT][hapmap]
rs4680201	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs4680205	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs4680209	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680210	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680211	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs484663	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs500051	0.85[JPT][hapmap]
rs517971	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs536008	0.91[JPT][hapmap]
rs569813	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs578492	0.90[JPT][hapmap]
rs6440997	0.85[JPT][hapmap]
rs6440998	0.85[JPT][hapmap]
rs6441002	0.91[JPT][hapmap]
rs6441003	0.91[JPT][hapmap]
rs6441005	0.95[JPT][hapmap]
rs6441009	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6767886	0.91[JPT][hapmap]
rs6768777	0.90[JPT][hapmap]
rs6769807	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6779500	0.82[JPT][hapmap]
rs6793225	0.90[JPT][hapmap]
rs7609669	0.90[JPT][hapmap]
rs7620748	0.81[AMR][1000 genomes]
rs7629025	0.81[GIH][hapmap];0.91[JPT][hapmap]
rs7629557	0.90[JPT][hapmap]
rs7641141	0.91[JPT][hapmap]
rs9809924	0.89[JPT][hapmap]
rs9818926	0.95[JPT][hapmap]
rs9828161	0.91[JPT][hapmap]
rs9865998	0.91[JPT][hapmap]
rs9874559	0.90[JPT][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	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs173369	SLC33A1	cis	cerebellum	SCAN
rs173369	PLCH1	cis	Nerve Tibial	GTEx
rs173369	SLC33A1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155399800-155422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:155400600-155421000	Weak transcription	Fetal Intestine Small	intestine
3	chr3:155409000-155419200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:155409000-155419400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:155409200-155422200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:155411000-155420600	Weak transcription	Fetal Intestine Large	intestine
7	chr3:155412600-155422400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:155412600-155437400	Weak transcription	Pancreas	Pancrea
9	chr3:155413800-155432000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:155414000-155420600	Weak transcription	Brain Germinal Matrix	brain
11	chr3:155415000-155421200	Weak transcription	Stomach Mucosa	stomach
12	chr3:155415400-155419200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:155415600-155421400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:155417400-155421600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:155417800-155419400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:155418000-155421600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:155418400-155420200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:155418600-155420200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:155418600-155420200	Enhancers	A549	lung
20	chr3:155418600-155421200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:155418800-155419600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:155418800-155423400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:155418800-155423400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:155419000-155419200	Active TSS	Brain Angular Gyrus	brain
25	chr3:155419000-155419600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:155419000-155419800	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr3:155419000-155420200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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