Variant report

Variant	rs2334877
Chromosome Location	chr16:71833332-71833333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71832833..71836832-chr16:71876405..71879704,4	K562	blood:
2	chr16:71831763..71833409-chr16:71841752..71843561,2	MCF-7	breast:
3	chr16:71826988..71830438-chr16:71831436..71833598,3	K562	blood:
4	chr16:71831282..71834654-chr16:71840292..71844031,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10852503	0.80[EUR][1000 genomes]
rs11075894	0.84[EUR][1000 genomes]
rs11075898	0.85[EUR][1000 genomes]
rs11075901	0.81[ASW][hapmap];0.90[CEU][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs11075904	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11075905	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11862723	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.85[EUR][1000 genomes]
rs12923990	0.81[EUR][1000 genomes]
rs12929547	0.95[EUR][1000 genomes]
rs1392484	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1423983	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.84[EUR][1000 genomes]
rs2032918	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.85[EUR][1000 genomes]
rs2052584	0.84[EUR][1000 genomes]
rs2052585	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs2133773	0.96[EUR][1000 genomes]
rs2334880	0.80[EUR][1000 genomes]
rs4788548	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap]
rs4788550	0.90[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.84[EUR][1000 genomes]
rs4788553	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788557	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4788559	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4788823	0.81[EUR][1000 genomes]
rs4788828	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.82[EUR][1000 genomes]
rs4788830	0.84[EUR][1000 genomes]
rs6499526	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6499528	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap]
rs6499529	0.85[EUR][1000 genomes]
rs6499530	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.83[EUR][1000 genomes]
rs6499531	0.81[EUR][1000 genomes]
rs6499534	0.87[EUR][1000 genomes]
rs6499538	0.85[CEU][hapmap];1.00[CHD][hapmap];0.86[EUR][1000 genomes]
rs6499540	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7186112	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7187948	0.84[EUR][1000 genomes]
rs7188675	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs7193549	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs7195059	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.83[EUR][1000 genomes]
rs7201712	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202479	0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7204118	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7204608	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.95[MKK][hapmap]
rs7204967	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7204992	0.80[EUR][1000 genomes]
rs7206470	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.80[EUR][1000 genomes]
rs7359478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8044144	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8051968	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8052910	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8053186	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8053745	0.83[EUR][1000 genomes]
rs8055419	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8062188	0.84[EUR][1000 genomes]
rs889568	0.87[EUR][1000 genomes]
rs9302630	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9635524	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs979790	1.00[CHD][hapmap]
rs9888756	0.83[EUR][1000 genomes]
rs9929840	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9929985	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9930015	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9934301	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs9937511	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9939458	0.90[CEU][hapmap]

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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2334877	PHLPPL	cis	multi-tissue	Pritchard
rs2334877	PHLPP2	cis	Muscle Skeletal	GTEx
rs2334877	COG4	cis	parietal	SCAN
rs2334877	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx
rs2334877	RANBP10	cis	parietal	SCAN
rs2334877	CTCF	cis	cerebellum	SCAN
rs2334877	NRN1L	cis	parietal	SCAN
rs2334877	B3GNT9	cis	parietal	SCAN
rs2334877	ZNF23	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71779600-71841800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:71816000-71840400	Weak transcription	Fetal Kidney	kidney
3	chr16:71821400-71840000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr16:71823200-71835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr16:71823200-71840400	Weak transcription	HUVEC	blood vessel
6	chr16:71823200-71841400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr16:71823400-71834800	Weak transcription	Small Intestine	intestine
8	chr16:71823400-71836000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr16:71823400-71836800	Weak transcription	Brain Germinal Matrix	brain
10	chr16:71823400-71837400	Weak transcription	HSMM	muscle
11	chr16:71823400-71838600	Weak transcription	Brain Substantia Nigra	brain
12	chr16:71823400-71839800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr16:71823400-71840000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:71823400-71840000	Weak transcription	Brain Angular Gyrus	brain
15	chr16:71823400-71840000	Weak transcription	Brain Anterior Caudate	brain
16	chr16:71823400-71840000	Weak transcription	K562	blood
17	chr16:71823400-71840200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr16:71823400-71840200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr16:71823400-71840400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr16:71823400-71840400	Weak transcription	Fetal Brain Male	brain
21	chr16:71823400-71840400	Weak transcription	NH-A	brain
22	chr16:71823400-71841000	Weak transcription	Colonic Mucosa	Colon
23	chr16:71823400-71841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr16:71823400-71841400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr16:71823400-71841400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr16:71823400-71841600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr16:71823400-71841600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr16:71823400-71841600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr16:71823400-71841600	Weak transcription	Aorta	Aorta
30	chr16:71823400-71841800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:71823400-71841800	Weak transcription	Esophagus	oesophagus
32	chr16:71823400-71841800	Weak transcription	Pancreas	Pancrea
33	chr16:71823600-71838800	Weak transcription	Hela-S3	cervix
34	chr16:71823600-71839600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr16:71823600-71840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr16:71823600-71840400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr16:71823800-71837600	Weak transcription	Osteobl	bone
38	chr16:71823800-71840800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr16:71825600-71839600	Weak transcription	Brain Hippocampus Middle	brain
40	chr16:71826400-71839600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr16:71826400-71840200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr16:71826600-71840400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:71826600-71840400	Weak transcription	Right Ventricle	heart
44	chr16:71826800-71833600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr16:71827000-71840200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr16:71827000-71841000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr16:71827000-71841000	Weak transcription	Right Atrium	heart
48	chr16:71827000-71841800	Weak transcription	Spleen	Spleen
49	chr16:71827400-71841200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr16:71827600-71840200	Weak transcription	NHEK	skin

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