Variant report

Variant	rs2862874
Chromosome Location	chr2:58990485-58990486
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	chr2:58989693..58992131-chr7:34155644..34158219,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10165014	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10193538	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10204566	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12986742	0.88[ASN][1000 genomes]
rs1613599	0.83[ASN][1000 genomes]
rs2862872	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2862873	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6419632	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545701	0.84[ASN][1000 genomes]
rs6545702	0.82[ASN][1000 genomes]
rs6723486	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6731121	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6748058	0.82[ASN][1000 genomes]
rs6759519	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6759757	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs727856	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs727857	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596101	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7597839	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963537	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv431180	chr2:58857542-59178687	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2862874	LOC339803	cis	parietal	SCAN
rs2862874	USP34	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58985600-58991600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:58988400-58991600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:58988600-58991000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:58989200-58990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:58989200-58990600	Enhancers	Primary hematopoietic stem cells	blood
6	chr2:58989400-58993000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:58989600-58990800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:58989800-58991800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:58989800-58992000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:58989800-58995000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:58990000-58991600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:58990200-58991600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:58990200-58991600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:58990200-58991800	Weak transcription	K562	blood
15	chr2:58990200-58995200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:58990400-58990600	Enhancers	H9 Cell Line	embryonic stem cell
17	chr2:58990400-58992000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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