Variant report

Variant	rs12928939
Chromosome Location	chr16:71800045-71800046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71795022..71797414-chr16:71798658..71803314,4	MCF-7	breast:
2	chr16:71792577..71794560-chr16:71799391..71801593,2	MCF-7	breast:
3	chr16:71799645..71801237-chr16:71841138..71842836,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10500560	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs11075903	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640830	0.85[ASN][1000 genomes]
rs11641113	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11642526	0.92[ASN][1000 genomes]
rs11642529	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11645704	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11645725	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11648483	0.85[ASN][1000 genomes]
rs11861296	0.86[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11865456	0.82[GIH][hapmap]
rs12149307	0.82[GIH][hapmap]
rs12149460	0.85[CEU][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12445161	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12445564	0.82[GIH][hapmap]
rs12445641	0.82[GIH][hapmap]
rs12446005	0.90[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs12447094	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12448022	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]
rs12919271	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12933007	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935106	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345868	0.90[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs17355804	0.83[LWK][hapmap]
rs17357420	0.96[GIH][hapmap]
rs34053338	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34358623	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34531032	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34680964	0.90[CEU][hapmap];0.96[GIH][hapmap];0.86[TSI][hapmap]
rs34731378	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34998650	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35706035	0.89[ASN][1000 genomes]
rs3751820	0.82[GIH][hapmap]
rs4528577	0.82[GIH][hapmap]
rs4788450	1.00[CHB][hapmap]
rs71386932	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188591	0.82[GIH][hapmap]
rs7190257	1.00[JPT][hapmap]
rs7195988	0.82[GIH][hapmap]
rs7197104	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197486	0.82[GIH][hapmap]
rs7198834	0.96[GIH][hapmap]
rs7202840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7205340	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs8049163	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8050058	0.96[GIH][hapmap]
rs8051878	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052358	0.96[GIH][hapmap]
rs8057568	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940234	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	esv1819402	chr16:71755852-71816899	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
5	esv1815957	chr16:71790812-71816899	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12928939	PHLPP2	cis	lymphoblastoid	seeQTL
rs12928939	PHLPP2	cis	cerebellum	SCAN
rs12928939	NRN1L	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71761000-71805600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:71762200-71811400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:71763200-71812600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr16:71763400-71802200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr16:71763600-71801400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr16:71763600-71812400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr16:71763800-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr16:71764000-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr16:71764000-71813000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr16:71764800-71802600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr16:71770800-71810600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr16:71770800-71813800	Strong transcription	Liver	Liver
13	chr16:71771000-71812200	Strong transcription	Placenta	Placenta
14	chr16:71779600-71841800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:71780000-71821400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr16:71783800-71820600	Weak transcription	Psoas Muscle	Psoas
17	chr16:71784000-71811200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:71785400-71808800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr16:71786400-71802200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr16:71786400-71805200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr16:71786600-71809800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr16:71787000-71802200	Strong transcription	Fetal Thymus	thymus
23	chr16:71788000-71806600	Weak transcription	Stomach Mucosa	stomach
24	chr16:71789800-71802200	Strong transcription	GM12878-XiMat	blood
25	chr16:71792600-71801000	Weak transcription	Fetal Brain Female	brain
26	chr16:71792600-71806600	Weak transcription	Fetal Brain Male	brain
27	chr16:71792800-71801600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:71792800-71803400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr16:71792800-71805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr16:71792800-71809600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr16:71792800-71811000	Weak transcription	Small Intestine	intestine
32	chr16:71793200-71808800	Strong transcription	Fetal Intestine Large	intestine
33	chr16:71793200-71830400	Weak transcription	Fetal Heart	heart
34	chr16:71794000-71808600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr16:71794600-71800800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr16:71794600-71802200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr16:71794800-71802200	Strong transcription	Dnd41	blood
38	chr16:71795000-71802200	Strong transcription	Primary B cells from cord blood	blood
39	chr16:71796800-71802200	Strong transcription	HSMM	muscle
40	chr16:71796800-71804200	Weak transcription	Colon Smooth Muscle	Colon
41	chr16:71797000-71800600	Weak transcription	Brain Angular Gyrus	brain
42	chr16:71797000-71801400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr16:71797000-71803000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:71797000-71804400	Weak transcription	Left Ventricle	heart
45	chr16:71797000-71804400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr16:71797000-71807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr16:71797000-71807200	Weak transcription	Esophagus	oesophagus
48	chr16:71797000-71807200	Weak transcription	Gastric	stomach
49	chr16:71797000-71807200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr16:71797000-71807200	Weak transcription	NHLF	lung

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