Variant report

Variant	rs518972
Chromosome Location	chr3:136039268-136039269
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10935177	0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10935181	0.84[ASN][1000 genomes]
rs10935182	1.00[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap]
rs10935183	0.92[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs10935184	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1145106	0.93[JPT][hapmap]
rs1153877	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1154988	0.86[JPT][hapmap]
rs11715257	0.93[JPT][hapmap]
rs11717954	1.00[ASW][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs12488721	0.82[ASN][1000 genomes]
rs12492510	1.00[ASW][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap]
rs1279086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1279424	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1279425	1.00[JPT][hapmap]
rs1279831	0.92[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap]
rs1279840	1.00[JPT][hapmap]
rs1279949	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1394092	1.00[JPT][hapmap]
rs1711161	0.93[JPT][hapmap]
rs1711170	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1711171	1.00[JPT][hapmap]
rs2655008	0.93[JPT][hapmap]
rs3755636	1.00[JPT][hapmap]
rs3957816	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs4678428	1.00[JPT][hapmap]
rs480162	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs480330	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs483465	1.00[JPT][hapmap]
rs517319	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs521746	1.00[ASW][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs527888	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548288	1.00[JPT][hapmap]
rs553018	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556788	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570621	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs571513	1.00[JPT][hapmap]
rs576771	0.93[JPT][hapmap]
rs589092	0.89[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs595532	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs606725	1.00[JPT][hapmap]
rs619605	0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs645040	0.86[JPT][hapmap]
rs650326	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654237	1.00[ASW][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs655836	1.00[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs661739	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs664088	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs667920	1.00[JPT][hapmap]
rs6791611	0.92[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs681783	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs684195	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs684773	0.86[JPT][hapmap]
rs687339	0.86[JPT][hapmap]
rs695983	0.93[JPT][hapmap]
rs696081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs696516	0.93[JPT][hapmap]
rs696518	1.00[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs696520	1.00[ASW][hapmap];0.85[CEU][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698270	0.93[JPT][hapmap]
rs699165	1.00[JPT][hapmap]
rs711972	0.82[ASN][1000 genomes]
rs711975	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap]
rs7372313	0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs7620314	0.92[CHB][hapmap]
rs834304	0.80[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes]
rs834305	0.81[ASN][1000 genomes]
rs838202	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs864437	1.00[ASW][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap]
rs866758	0.92[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs895894	0.89[CHD][hapmap];0.86[JPT][hapmap]
rs900048	0.93[JPT][hapmap]
rs9840812	0.86[JPT][hapmap]
rs9845457	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9854084	1.00[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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4025	chr3:136017458-136065622	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs518972	PCCB	cis	cerebellum	SCAN
rs518972	DBR1	cis	cerebellum	SCAN
rs518972	PCCB	cis	lymphoblastoid	seeQTL
rs518972	SPSB4	cis	cerebellum	SCAN
rs518972	PCCB	cis	multi-tissue	Pritchard
rs518972	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs518972	PCCB	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135981200-136052000	Weak transcription	NH-A	brain
3	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
5	chr3:136014200-136040000	Weak transcription	Small Intestine	intestine
6	chr3:136016800-136045600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:136017000-136040000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:136018200-136051400	Weak transcription	A549	lung
9	chr3:136020200-136040200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:136020200-136045200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:136020400-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:136020400-136045200	Weak transcription	Colonic Mucosa	Colon
13	chr3:136020600-136045000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:136020600-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:136020800-136040200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:136020800-136040200	Weak transcription	Esophagus	oesophagus
17	chr3:136020800-136042200	Weak transcription	Placenta	Placenta
18	chr3:136020800-136043000	Weak transcription	HSMM	muscle
19	chr3:136020800-136045000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:136021000-136040000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:136021000-136045400	Weak transcription	Gastric	stomach
22	chr3:136021000-136045600	Weak transcription	Osteobl	bone
23	chr3:136021200-136039800	Weak transcription	NHEK	skin
24	chr3:136021200-136040000	Weak transcription	Thymus	Thymus
25	chr3:136030600-136040200	Weak transcription	Pancreas	Pancrea
26	chr3:136032800-136055400	Weak transcription	HUVEC	blood vessel
27	chr3:136035600-136040200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:136035600-136040600	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:136036400-136044200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:136036800-136040000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:136036800-136043400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:136037000-136040400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:136037000-136041600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr3:136037000-136045200	Weak transcription	Brain Angular Gyrus	brain
35	chr3:136037200-136040000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:136037200-136040200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:136037200-136040200	Weak transcription	Lung	lung
38	chr3:136037200-136045200	Weak transcription	Fetal Stomach	stomach
39	chr3:136037600-136039400	ZNF genes & repeats	Fetal Brain Female	brain
40	chr3:136037600-136045200	Weak transcription	K562	blood
41	chr3:136037600-136045400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:136037800-136041000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:136037800-136042200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:136038000-136040000	Weak transcription	Ovary	ovary
45	chr3:136038000-136042600	ZNF genes & repeats	Dnd41	blood
46	chr3:136038200-136039400	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr3:136038200-136039600	ZNF genes & repeats	HepG2	liver
48	chr3:136038200-136040000	ZNF genes & repeats	Fetal Brain Male	brain
49	chr3:136038200-136040200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
50	chr3:136038200-136040600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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