Variant report

Variant	rs2015945
Chromosome Location	chr3:155414430-155414431
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	chr3:155100662..155102624-chr3:155412675..155414490,2	MCF-7	breast:
2	chr3:155409079..155411768-chr3:155413366..155415925,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10936006	0.81[JPT][hapmap]
rs10936014	0.82[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12053896	0.82[CHB][hapmap]
rs12632699	0.91[JPT][hapmap]
rs1401695	0.90[JPT][hapmap]
rs1607590	0.90[JPT][hapmap]
rs1607591	0.91[JPT][hapmap]
rs173369	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]
rs181696	0.86[JPT][hapmap]
rs183088	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]
rs1878859	0.89[JPT][hapmap]
rs1879089	0.91[JPT][hapmap]
rs189639	0.91[JPT][hapmap]
rs1914799	0.91[JPT][hapmap]
rs193313	0.86[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2102897	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2203885	0.95[JPT][hapmap]
rs2315589	0.95[JPT][hapmap]
rs2315590	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs358705	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs358726	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs358729	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs358908	0.82[JPT][hapmap]
rs358909	0.82[JPT][hapmap]
rs359539	0.90[JPT][hapmap]
rs359540	0.91[JPT][hapmap]
rs359542	0.86[JPT][hapmap]
rs359549	0.91[JPT][hapmap]
rs359551	0.91[JPT][hapmap]
rs359552	0.91[JPT][hapmap]
rs359553	0.91[JPT][hapmap]
rs359554	0.91[JPT][hapmap]
rs359556	0.91[JPT][hapmap]
rs359557	0.91[JPT][hapmap]
rs359561	0.91[JPT][hapmap]
rs359565	0.89[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs359566	0.91[JPT][hapmap]
rs359568	0.91[JPT][hapmap]
rs359569	0.91[JPT][hapmap]
rs359570	0.91[JPT][hapmap]
rs3908138	0.91[JPT][hapmap]
rs3908140	0.91[JPT][hapmap]
rs3908141	0.91[JPT][hapmap]
rs3908144	0.90[JPT][hapmap]
rs3914780	0.91[JPT][hapmap]
rs407033	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410115	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4125975	0.91[JPT][hapmap]
rs416494	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4287944	0.95[JPT][hapmap]
rs4401403	0.91[JPT][hapmap]
rs4680201	0.91[JPT][hapmap]
rs4680205	0.91[JPT][hapmap]
rs4680209	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680210	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]
rs4680211	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs484663	0.91[JPT][hapmap]
rs500051	0.85[JPT][hapmap]
rs517971	0.91[JPT][hapmap]
rs536008	0.91[JPT][hapmap]
rs569813	0.91[JPT][hapmap]
rs578492	0.91[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	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6767886	0.91[JPT][hapmap]
rs6768777	0.90[JPT][hapmap]
rs6769807	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6779500	0.83[JPT][hapmap]
rs6793225	0.91[JPT][hapmap]
rs7609669	0.90[JPT][hapmap]
rs7620748	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7629025	0.91[JPT][hapmap]
rs7629557	0.90[JPT][hapmap]
rs7641141	0.91[JPT][hapmap]
rs9809924	0.90[JPT][hapmap]
rs9818926	0.95[JPT][hapmap]
rs9828161	0.91[JPT][hapmap]
rs9865998	0.91[JPT][hapmap]
rs9874559	0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2015945	PLCH1	cis	Nerve Tibial	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155395000-155416800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:155399800-155422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:155400600-155421000	Weak transcription	Fetal Intestine Small	intestine
4	chr3:155400800-155418400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:155408800-155416400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:155408800-155418600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:155409000-155419200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:155409000-155419400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:155409200-155418400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:155409200-155422200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:155411000-155420600	Weak transcription	Fetal Intestine Large	intestine
12	chr3:155412600-155422400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:155412600-155437400	Weak transcription	Pancreas	Pancrea
14	chr3:155413800-155432000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:155414000-155418600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:155414000-155420600	Weak transcription	Brain Germinal Matrix	brain
17	chr3:155414400-155414800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:155414400-155415600	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links