Variant report

Variant	rs7205340
Chromosome Location	chr16:71645670-71645671
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71644641..71645674-chr16:71679043..71680015,5	MCF-7	breast:
2	chr16:71598501..71600044-chr16:71644493..71645682,11	MCF-7	breast:
3	chr16:71567921..71569617-chr16:71645011..71646646,2	MCF-7	breast:
4	chr16:71645006..71646699-chr16:71648502..71650487,2	MCF-7	breast:
5	chr16:71645072..71647361-chr16:71660009..71661728,2	MCF-7	breast:
6	chr16:71596573..71599590-chr16:71642907..71646466,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252339	Chromatin interaction
ENSG00000140832	Chromatin interaction
ENSG00000157429	Chromatin interaction
ENSG00000260593	Chromatin interaction
ENSG00000260886	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10500560	0.93[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1056303	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11639902	0.92[ASW][hapmap];0.82[CEU][hapmap];0.86[LWK][hapmap]
rs11640830	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11641967	0.82[CHB][hapmap]
rs11642529	1.00[JPT][hapmap]
rs11645598	0.82[CHB][hapmap]
rs11648483	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11670	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11861513	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12445161	0.81[EUR][1000 genomes]
rs12446005	0.93[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448022	0.93[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12924631	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12928939	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs1345868	0.93[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34028112	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34358623	0.82[EUR][1000 genomes]
rs34680964	0.93[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34731378	0.81[EUR][1000 genomes]
rs61733127	0.83[ASN][1000 genomes]
rs61753635	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71403864	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7185575	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7190257	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7192860	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202840	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs8046629	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8049163	0.93[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8051878	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs8053623	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv3430225	chr16:71633500-71661205	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7205340	PHLPP2	cis	lymphoblastoid	seeQTL
rs7205340	PHLPP2	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71644200-71647600	Weak transcription	Right Atrium	heart
2	chr16:71644800-71645800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr16:71644800-71645800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr16:71644800-71646000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr16:71645000-71645800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr16:71645200-71646000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr16:71645400-71645800	Enhancers	Liver	Liver
8	chr16:71645600-71645800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr16:71645600-71645800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
10	chr16:71645600-71645800	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr16:71645600-71645800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr16:71645600-71647000	Enhancers	HepG2	liver

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