Variant report

Variant	rs12448022
Chromosome Location	chr16:71724369-71724370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71723824..71726811-chr16:71728451..71731387,3	MCF-7	breast:
2	chr16:71723301..71725915-chr16:71755772..71758292,2	MCF-7	breast:
3	chr16:71722834..71724416-chr16:71742268..71745053,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261513	Chromatin interaction
ENSG00000040199	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10500560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10500567	1.00[CHB][hapmap]
rs1056303	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10852505	1.00[CHB][hapmap]
rs11075903	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11639902	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs11640830	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11641113	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11642526	0.92[ASN][1000 genomes]
rs11642529	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11645704	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11645725	0.83[EUR][1000 genomes]
rs11648483	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11861296	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs12445161	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12446005	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12447094	0.85[EUR][1000 genomes]
rs12919271	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12924631	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12928939	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12933007	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12935106	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1345868	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17357420	1.00[CHB][hapmap];0.96[GIH][hapmap]
rs2288030	1.00[CHB][hapmap]
rs2878494	1.00[CHB][hapmap]
rs34028112	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34358623	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34680964	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34731378	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34998650	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35706035	0.89[ASN][1000 genomes]
rs4788568	1.00[CHB][hapmap]
rs61753635	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71386932	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71403864	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7185575	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7190257	1.00[JPT][hapmap]
rs7192860	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7197104	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7198834	0.96[GIH][hapmap]
rs7202840	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7205340	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]
rs8046629	0.82[AFR][1000 genomes]
rs8049163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051878	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8052358	0.96[GIH][hapmap]
rs8053623	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8057568	0.84[EUR][1000 genomes];0.85[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	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
4	esv1817133	chr16:71705908-71837477	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12448022	PHLPP2	cis	lymphoblastoid	seeQTL
rs12448022	PHLPP2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71672000-71741400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:71683800-71756600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:71685200-71741200	Weak transcription	Psoas Muscle	Psoas
4	chr16:71685800-71726000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr16:71687800-71725000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:71690600-71733600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr16:71690600-71741200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr16:71690800-71725600	Weak transcription	Fetal Thymus	thymus
9	chr16:71693000-71756400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr16:71695000-71725200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:71695000-71726000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr16:71695200-71724800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:71695200-71725200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr16:71696400-71725200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr16:71702000-71756200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr16:71705000-71741600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr16:71705000-71756200	Weak transcription	Colon Smooth Muscle	Colon
18	chr16:71705000-71756800	Weak transcription	Gastric	stomach
19	chr16:71705200-71732200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr16:71705400-71733000	Weak transcription	Pancreas	Pancrea
21	chr16:71707400-71750200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr16:71710400-71735800	Weak transcription	Right Ventricle	heart
23	chr16:71710600-71726600	Weak transcription	Fetal Brain Male	brain
24	chr16:71710600-71732200	Weak transcription	Thymus	Thymus
25	chr16:71710600-71741800	Weak transcription	Spleen	Spleen
26	chr16:71710600-71756200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:71710600-71756400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr16:71710600-71756800	Weak transcription	Lung	lung
29	chr16:71711200-71756400	Weak transcription	K562	blood
30	chr16:71712400-71724800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:71713200-71734800	Weak transcription	Placenta	Placenta
32	chr16:71713400-71732200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr16:71713400-71739800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr16:71713400-71741600	Weak transcription	NHLF	lung
35	chr16:71714600-71733200	Weak transcription	Brain Germinal Matrix	brain
36	chr16:71715800-71726000	Weak transcription	Small Intestine	intestine
37	chr16:71715800-71732200	Weak transcription	NHEK	skin
38	chr16:71715800-71741200	Weak transcription	Hela-S3	cervix
39	chr16:71715800-71756000	Weak transcription	Brain Hippocampus Middle	brain
40	chr16:71716600-71732800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr16:71716800-71756600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr16:71717200-71725200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr16:71718400-71725200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr16:71718800-71732200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr16:71718800-71732200	Weak transcription	Aorta	Aorta
46	chr16:71719000-71739800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr16:71719800-71725000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr16:71720200-71733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr16:71720400-71724800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr16:71720600-71724800	Strong transcription	Muscle Satellite Cultured Cells	--

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