Variant report

Variant	rs480162
Chromosome Location	chr3:136068695-136068696
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10935181	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10935182	0.90[EUR][1000 genomes]
rs10935184	0.86[EUR][1000 genomes]
rs1153877	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11717954	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11915629	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1279086	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1279424	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1279949	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs480330	0.81[ASN][1000 genomes]
rs517319	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs518972	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs521746	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs527888	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs553018	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs556788	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56235965	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs570621	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs619605	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs650326	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs654237	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655836	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs664088	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66691851	0.81[EUR][1000 genomes]
rs6791611	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs681783	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs684195	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs696081	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs696518	0.84[ASN][1000 genomes]
rs696520	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698269	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs711972	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73222302	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs834304	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs834305	0.84[ASN][1000 genomes]
rs838202	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs864437	0.86[ASN][1000 genomes]
rs866758	0.84[ASN][1000 genomes]

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	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
4	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs480162	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs480162	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136039000-136072400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:136042400-136078800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:136042600-136072600	Strong transcription	Dnd41	blood
4	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
5	chr3:136043600-136082000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:136043800-136070400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:136045600-136079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:136047800-136074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:136051000-136069800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:136051600-136069200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:136051600-136070800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:136052200-136069200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:136052800-136070800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:136053000-136072400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:136053800-136069000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:136054200-136085400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:136054600-136074200	Weak transcription	Brain Angular Gyrus	brain
19	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:136054800-136076600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:136055400-136069000	Weak transcription	Aorta	Aorta
22	chr3:136055600-136073400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:136055600-136100800	Weak transcription	Spleen	Spleen
24	chr3:136057800-136069800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:136059000-136072000	Weak transcription	GM12878-XiMat	blood
26	chr3:136059200-136069200	Weak transcription	Psoas Muscle	Psoas
27	chr3:136059600-136070400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:136059600-136079000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:136060400-136069200	Weak transcription	Right Ventricle	heart
30	chr3:136061800-136074200	Weak transcription	Brain Germinal Matrix	brain
31	chr3:136063200-136071000	Weak transcription	Fetal Brain Female	brain
32	chr3:136063200-136072200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:136063400-136068800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:136063400-136069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:136063400-136069000	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:136063400-136069000	Weak transcription	Fetal Heart	heart
37	chr3:136063400-136069000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:136063400-136069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:136063400-136069000	Weak transcription	Thymus	Thymus
40	chr3:136063400-136069200	Weak transcription	Esophagus	oesophagus
41	chr3:136063400-136069200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:136063400-136069200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:136063400-136071800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:136063400-136072200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:136063400-136072200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:136063400-136073800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:136063600-136068800	Weak transcription	Left Ventricle	heart
50	chr3:136063600-136068800	Weak transcription	HMEC	breast

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