Variant report

Variant	rs172650
Chromosome Location	chr16:71603912-71603913
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71598954..71602131-chr16:71602948..71606674,3	K562	blood:
2	chr16:71596326..71598942-chr16:71602186..71604284,2	K562	blood:
3	chr16:71596888..71600063-chr16:71602973..71605498,3	MCF-7	breast:

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

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1035545	0.87[CEU][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs10500559	0.83[ASN][1000 genomes]
rs1058747	0.87[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs11075889	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11075890	0.91[ASN][1000 genomes]
rs11075891	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11075892	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11075895	0.82[CHD][hapmap];0.83[GIH][hapmap]
rs11539980	0.87[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs11643690	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11648240	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11648674	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs11859729	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs11862798	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12051443	0.82[ASN][1000 genomes]
rs12051506	0.83[ASN][1000 genomes]
rs12444484	0.87[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12447856	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs12597065	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs12920243	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs12927320	0.82[ASN][1000 genomes]
rs12930206	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs12932850	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1392487	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs1477386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1582589	0.87[CEU][hapmap];0.82[ASN][1000 genomes]
rs16973266	0.82[JPT][hapmap]
rs172649	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032920	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2036338	0.87[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs2113222	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2270830	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs2270831	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs2270832	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs2278031	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs2303224	0.82[ASN][1000 genomes]
rs2303225	0.91[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs2334879	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2334883	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2334884	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432519	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432520	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432524	0.94[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs310331	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34764568	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35939203	0.88[ASN][1000 genomes]
rs3752681	0.87[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs3829537	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4444347	0.83[JPT][hapmap]
rs4788544	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4788546	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788547	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4788549	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs4788551	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs4788808	0.82[CHD][hapmap]
rs4788809	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4788812	0.96[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788814	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4788817	0.96[CEU][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4788821	0.87[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4788826	0.86[CEU][hapmap];0.88[JPT][hapmap]
rs4788827	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs62053077	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62053078	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62053107	0.82[ASN][1000 genomes]
rs7185997	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs7186717	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7188406	0.93[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[ASN][1000 genomes]
rs7195840	0.87[ASN][1000 genomes]
rs7201754	0.83[GIH][hapmap];0.83[JPT][hapmap]
rs7202288	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs7206039	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8048057	0.87[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs8048210	0.87[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs8060867	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs8061970	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs8203	0.87[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs918721	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap]
rs979789	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap]
rs9921270	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs9923264	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9923336	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9925228	0.87[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs9930543	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9932415	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9933961	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9939455	0.87[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs9939471	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9939658	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9940142	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9940217	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs9940707	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs172650	PHLPP2	cis	lymphoblastoid	seeQTL
rs172650	PHLPPL	cis	multi-tissue	Pritchard
rs172650	NFKBIE	trans	brain	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71599600-71605600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr16:71599600-71607800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:71600400-71604000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr16:71600600-71606000	Weak transcription	Fetal Intestine Large	intestine
5	chr16:71600600-71606000	Weak transcription	A549	lung
6	chr16:71602400-71615400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:71603400-71604000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr16:71603400-71604000	Enhancers	HepG2	liver
9	chr16:71603600-71604600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr16:71603600-71604600	Genic enhancers	Liver	Liver
11	chr16:71603600-71605800	Weak transcription	Fetal Intestine Small	intestine

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