Variant report

Variant	rs4680210
Chromosome Location	chr3:155384469-155384470
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155383548..155385347-chr3:155462501..155464169,2	K562	blood:
2	chr3:155379377..155381344-chr3:155382651..155384726,2	K562	blood:

Variant related genes	Relation type
ENSG00000114805	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10936014	0.82[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12632699	0.86[JPT][hapmap]
rs1401695	0.85[JPT][hapmap]
rs1607590	0.85[JPT][hapmap]
rs1607591	0.86[JPT][hapmap]
rs173369	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]
rs181696	0.81[JPT][hapmap]
rs183088	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.92[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]
rs1878859	0.83[JPT][hapmap]
rs1879089	0.86[JPT][hapmap]
rs189639	0.86[JPT][hapmap]
rs1914799	0.87[GIH][hapmap];0.86[JPT][hapmap]
rs193313	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2015945	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2102897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2203885	0.91[JPT][hapmap]
rs2315589	0.91[JPT][hapmap];0.88[LWK][hapmap]
rs2315590	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs358705	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs358726	0.80[CHB][hapmap]
rs358900	0.84[ASN][1000 genomes]
rs359539	0.86[JPT][hapmap]
rs359540	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs359542	0.81[JPT][hapmap]
rs359549	0.87[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap]
rs359551	0.86[JPT][hapmap]
rs359552	0.86[JPT][hapmap]
rs359553	0.86[JPT][hapmap]
rs359554	0.86[JPT][hapmap]
rs359556	0.86[JPT][hapmap]
rs359557	0.86[JPT][hapmap]
rs359561	0.85[JPT][hapmap]
rs359565	0.89[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs359566	0.86[JPT][hapmap]
rs359568	0.86[JPT][hapmap]
rs359569	0.86[JPT][hapmap]
rs359570	0.86[JPT][hapmap]
rs3908138	0.86[JPT][hapmap]
rs3908140	0.86[JPT][hapmap]
rs3908141	0.87[GIH][hapmap];0.86[JPT][hapmap]
rs3908144	0.90[JPT][hapmap]
rs3914780	0.86[JPT][hapmap]
rs407033	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs410115	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4125975	0.86[JPT][hapmap]
rs416494	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4287944	0.89[JPT][hapmap]
rs4401403	0.86[JPT][hapmap]
rs4680201	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs4680205	0.87[GIH][hapmap];0.86[JPT][hapmap]
rs4680209	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680211	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs484663	0.87[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap]
rs500051	0.81[JPT][hapmap];0.83[LWK][hapmap]
rs517971	0.87[GIH][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap]
rs536008	0.86[JPT][hapmap]
rs569813	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs578492	0.86[JPT][hapmap]
rs6440998	0.80[JPT][hapmap]
rs6441002	0.86[JPT][hapmap]
rs6441003	0.86[JPT][hapmap]
rs6441005	0.91[JPT][hapmap]
rs6441009	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767886	0.86[JPT][hapmap]
rs6768777	0.85[JPT][hapmap]
rs6769807	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6793225	0.86[JPT][hapmap]
rs7609669	0.86[JPT][hapmap]
rs7620748	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7629025	0.87[GIH][hapmap];0.86[JPT][hapmap]
rs7629557	0.85[JPT][hapmap]
rs7641141	0.86[JPT][hapmap]
rs9809924	0.84[JPT][hapmap]
rs9818926	0.90[JPT][hapmap]
rs9828161	0.86[JPT][hapmap]
rs9865998	0.86[JPT][hapmap]
rs9874559	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4680210	SLC33A1	cis	parietal	SCAN
rs4680210	SLC33A1	cis	cerebellum	SCAN
rs4680210	MLF1	cis	parietal	SCAN
rs4680210	PLCH1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155378800-155385400	Enhancers	Fetal Intestine Large	intestine
2	chr3:155381200-155386200	Enhancers	Fetal Intestine Small	intestine
3	chr3:155382800-155385200	Enhancers	Stomach Mucosa	stomach
4	chr3:155383400-155384600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:155383400-155385000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:155383400-155385200	Enhancers	Duodenum Mucosa	Duodenum
7	chr3:155383400-155385600	Weak transcription	Brain Anterior Caudate	brain
8	chr3:155383400-155387000	Enhancers	HepG2	liver
9	chr3:155383400-155390200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:155383400-155393800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:155383400-155394000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:155383400-155395800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:155383600-155384600	Weak transcription	Small Intestine	intestine
14	chr3:155383600-155394000	Weak transcription	Pancreas	Pancrea
15	chr3:155384000-155385200	Enhancers	A549	lung
16	chr3:155384400-155384600	Enhancers	Rectal Mucosa Donor 31	rectum

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