Variant report

Variant	rs10500560
Chromosome Location	chr16:71681153-71681154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71658774..71660870-chr16:71677637..71681268,4	MCF-7	breast:
2	chr16:71678612..71682239-chr16:71682630..71684889,3	K562	blood:

Variant related genes	Relation type
ENSG00000140832	Chromatin interaction
ENSG00000260593	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1056303	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11639902	1.00[ASW][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]
rs11640830	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11641967	1.00[CHB][hapmap]
rs11642529	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs11648483	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11861296	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs11861513	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs12445161	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12446005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12447094	0.80[EUR][1000 genomes]
rs12448022	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]
rs12919271	0.81[EUR][1000 genomes]
rs12924631	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12928939	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1345868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17345313	0.82[CHB][hapmap]
rs34028112	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34358623	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34680964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34731378	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61733127	0.92[ASN][1000 genomes]
rs61753635	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71403864	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7185575	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7190257	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7192860	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7197104	0.81[EUR][1000 genomes]
rs7202840	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7205340	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]
rs8046629	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs8049163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8051878	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs8053623	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10500560	PHLPP2	cis	lymphoblastoid	seeQTL
rs10500560	PHLPP2	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71661800-71682000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:71662600-71682000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr16:71663600-71686600	Weak transcription	Small Intestine	intestine
4	chr16:71663800-71681400	Weak transcription	Left Ventricle	heart
5	chr16:71663800-71681400	Weak transcription	HepG2	liver
6	chr16:71664600-71682800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr16:71665200-71682800	Weak transcription	HMEC	breast
8	chr16:71668000-71703000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr16:71668200-71681800	Weak transcription	Spleen	Spleen
10	chr16:71669600-71681400	Weak transcription	Brain Angular Gyrus	brain
11	chr16:71669600-71681600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr16:71670000-71682600	Weak transcription	Brain Substantia Nigra	brain
13	chr16:71670200-71682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr16:71670400-71681400	Weak transcription	Fetal Muscle Leg	muscle
15	chr16:71670800-71681800	Weak transcription	Colon Smooth Muscle	Colon
16	chr16:71671200-71683200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:71671600-71686400	Weak transcription	Fetal Heart	heart
18	chr16:71671800-71682200	Weak transcription	Right Ventricle	heart
19	chr16:71671800-71704000	Weak transcription	Fetal Brain Male	brain
20	chr16:71672000-71681200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr16:71672000-71681400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr16:71672000-71681600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr16:71672000-71682600	Weak transcription	NHLF	lung
24	chr16:71672000-71682800	Weak transcription	NH-A	brain
25	chr16:71672000-71741400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr16:71672200-71681200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr16:71672200-71681400	Weak transcription	NHDF-Ad	bronchial
28	chr16:71672200-71681800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr16:71672200-71682600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr16:71672200-71682800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:71672400-71681200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr16:71672400-71682200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr16:71672400-71682800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr16:71672400-71686400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr16:71673000-71681400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr16:71673400-71682800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr16:71674600-71681400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr16:71674600-71681400	Weak transcription	NHEK	skin
39	chr16:71674600-71682000	Weak transcription	Liver	Liver
40	chr16:71674800-71681200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr16:71674800-71681400	Weak transcription	Brain Anterior Caudate	brain
42	chr16:71674800-71681800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr16:71674800-71682200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr16:71674800-71682800	Weak transcription	Gastric	stomach
45	chr16:71674800-71682800	Weak transcription	A549	lung
46	chr16:71674800-71704600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr16:71675000-71681200	Weak transcription	Brain Hippocampus Middle	brain
48	chr16:71675000-71681400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr16:71675000-71681400	Weak transcription	Brain Germinal Matrix	brain
50	chr16:71675000-71681400	Weak transcription	Pancreas	Pancrea

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