Variant report

Variant	rs1469908
Chromosome Location	chr16:69764412-69764413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69758127..69765240-chr16:69786072..69790209,13	K562	blood:
2	chr16:69762814..69765280-chr16:69787584..69790176,2	K562	blood:
3	chr16:69756715..69759145-chr16:69764152..69766520,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141101	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11640319	0.84[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs12596945	0.91[ASN][1000 genomes]
rs12599391	0.82[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs12918548	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12921782	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12924052	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12933210	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1364063	0.82[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs1437134	0.82[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs1837016	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2017448	0.83[AFR][1000 genomes]
rs2161630	0.84[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs244415	0.82[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs244417	0.82[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs244418	0.82[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs244420	0.82[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs2917670	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2917671	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2917678	0.95[ASN][1000 genomes]
rs2965749	0.84[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3811348	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3848278	0.84[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs45488899	0.87[ASN][1000 genomes]
rs4633710	0.83[JPT][hapmap];0.94[YRI][hapmap]
rs55780735	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6499241	0.82[AFR][1000 genomes]
rs6499244	0.89[YRI][hapmap]
rs6499251	0.82[ASN][1000 genomes]
rs7186296	0.84[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs7187634	0.84[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7189878	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs7191292	0.84[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs7192380	0.84[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7359336	0.82[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap]
rs8045432	0.81[AFR][1000 genomes]
rs8049728	0.84[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs8055756	0.84[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs8061052	0.92[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs9302604	0.81[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]

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	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	54 gene(s)	inside rSNPs	diseases
2	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv517207	chr16:69745145-69771914	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1469908	PLA2G15	cis	cerebellum	SCAN
rs1469908	CMTM1	cis	cerebellum	SCAN
rs1469908	LOC283970	cis	multi-tissue	Pritchard
rs1469908	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs1469908	PLEKHG4	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69761000-69773200	Weak transcription	Brain Germinal Matrix	brain
2	chr16:69761000-69773400	Weak transcription	Fetal Lung	lung
3	chr16:69761200-69772600	Weak transcription	Fetal Stomach	stomach
4	chr16:69761200-69773000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr16:69761200-69773000	Weak transcription	Fetal Brain Female	brain
6	chr16:69761200-69773000	Weak transcription	Fetal Intestine Large	intestine
7	chr16:69761200-69773200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr16:69761200-69773200	Weak transcription	Pancreas	Pancrea
9	chr16:69761200-69775400	Weak transcription	Fetal Brain Male	brain
10	chr16:69761200-69776200	Weak transcription	Ovary	ovary
11	chr16:69761400-69766200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr16:69761400-69773000	Weak transcription	Fetal Intestine Small	intestine
13	chr16:69761400-69773200	Weak transcription	Primary B cells from cord blood	blood
14	chr16:69761400-69773800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr16:69761400-69773800	Weak transcription	Placenta	Placenta
16	chr16:69761400-69774200	Weak transcription	Esophagus	oesophagus
17	chr16:69761400-69774200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr16:69761600-69773000	Weak transcription	Primary T cells from cord blood	blood
19	chr16:69761600-69773000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr16:69761600-69773800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:69761600-69773800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr16:69761600-69773800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr16:69761600-69774000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr16:69761600-69774000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr16:69761600-69774000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr16:69761600-69774200	Weak transcription	Colon Smooth Muscle	Colon
27	chr16:69761600-69774200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr16:69761800-69766200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr16:69761800-69770800	Weak transcription	HSMM	muscle
30	chr16:69761800-69773000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr16:69761800-69773000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr16:69761800-69773000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr16:69761800-69773000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr16:69761800-69773000	Weak transcription	Left Ventricle	heart
35	chr16:69761800-69773000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr16:69761800-69773400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr16:69761800-69773800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr16:69761800-69773800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr16:69761800-69773800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr16:69761800-69774000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr16:69761800-69774200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr16:69761800-69774200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr16:69761800-69774200	Weak transcription	Brain Substantia Nigra	brain
44	chr16:69761800-69774200	Weak transcription	NHEK	skin
45	chr16:69761800-69774200	Weak transcription	NHLF	lung
46	chr16:69761800-69774400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr16:69761800-69787400	Weak transcription	Right Atrium	heart
48	chr16:69762000-69771400	Weak transcription	HSMMtube	muscle
49	chr16:69762000-69773000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr16:69762000-69773000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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