Variant report

Variant	rs553018
Chromosome Location	chr3:136037227-136037228
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135915139..135916754-chr3:136035024..136037890,2	K562	blood:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10935177	0.92[CHB][hapmap]
rs10935181	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10935182	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs10935183	0.81[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap]
rs10935184	0.86[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs1145106	0.87[JPT][hapmap]
rs1153877	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715257	0.87[JPT][hapmap]
rs11717954	0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs12330635	0.86[JPT][hapmap]
rs12492510	0.81[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1279086	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]
rs1279424	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1279425	0.93[JPT][hapmap]
rs1279831	0.92[CHB][hapmap]
rs1279840	0.93[JPT][hapmap]
rs1279949	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1394092	0.93[JPT][hapmap]
rs1711161	0.81[JPT][hapmap]
rs1711170	0.81[ASN][1000 genomes]
rs1711171	0.93[JPT][hapmap]
rs2655008	0.87[JPT][hapmap]
rs3755636	0.93[JPT][hapmap]
rs4678428	0.93[JPT][hapmap]
rs480162	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs480330	0.96[ASN][1000 genomes]
rs483465	0.93[JPT][hapmap]
rs517319	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs518972	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]
rs521746	0.81[JPT][hapmap]
rs527888	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs548288	0.93[JPT][hapmap]
rs556788	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs570621	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs571513	0.93[JPT][hapmap]
rs576771	0.87[JPT][hapmap]
rs589092	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs595532	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs606725	0.93[JPT][hapmap]
rs619605	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs650326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs654237	0.83[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs655836	0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs664088	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667920	0.93[JPT][hapmap]
rs6791611	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs681783	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs684195	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs695983	0.87[JPT][hapmap]
rs696081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs696516	0.87[JPT][hapmap]
rs696518	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs696520	0.89[CEU][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698270	0.87[JPT][hapmap]
rs699165	0.93[JPT][hapmap]
rs711975	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs7372313	0.92[CHB][hapmap]
rs7620314	0.92[CHB][hapmap]
rs834304	0.81[CEU][hapmap];0.92[CHB][hapmap];0.82[AMR][1000 genomes]
rs838202	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs864437	0.80[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap]
rs866758	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs900048	0.87[JPT][hapmap]
rs9820485	0.86[JPT][hapmap]
rs9832056	0.86[JPT][hapmap]
rs9832813	0.86[JPT][hapmap]
rs9845457	0.83[CHB][hapmap]
rs9848883	0.86[JPT][hapmap]
rs9851986	0.86[JPT][hapmap]
rs9854084	0.93[JPT][hapmap]
rs9856769	0.86[JPT][hapmap]
rs9869720	0.85[JPT][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	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	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs553018	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs553018	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

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	chr3:135999800-136038200	Weak transcription	Fetal Brain Male	brain
5	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
6	chr3:136000200-136038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:136014200-136040000	Weak transcription	Small Intestine	intestine
8	chr3:136015000-136038800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:136016400-136038400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:136016800-136045600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:136017000-136040000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:136018200-136051400	Weak transcription	A549	lung
13	chr3:136019000-136038600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:136020200-136039000	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:136020200-136040200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:136020200-136045200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:136020400-136038400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:136020400-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:136020400-136045200	Weak transcription	Colonic Mucosa	Colon
20	chr3:136020600-136038000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:136020600-136038200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:136020600-136045000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:136020600-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:136020800-136037400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:136020800-136040200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:136020800-136040200	Weak transcription	Esophagus	oesophagus
27	chr3:136020800-136042200	Weak transcription	Placenta	Placenta
28	chr3:136020800-136043000	Weak transcription	HSMM	muscle
29	chr3:136020800-136045000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:136021000-136038600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:136021000-136038600	Weak transcription	Right Ventricle	heart
32	chr3:136021000-136038600	Weak transcription	GM12878-XiMat	blood
33	chr3:136021000-136038800	Weak transcription	Fetal Kidney	kidney
34	chr3:136021000-136040000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:136021000-136045400	Weak transcription	Gastric	stomach
36	chr3:136021000-136045600	Weak transcription	Osteobl	bone
37	chr3:136021200-136038200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:136021200-136038200	Weak transcription	Fetal Thymus	thymus
39	chr3:136021200-136038800	Weak transcription	HSMMtube	muscle
40	chr3:136021200-136039800	Weak transcription	NHEK	skin
41	chr3:136021200-136040000	Weak transcription	Thymus	Thymus
42	chr3:136026000-136038600	Weak transcription	Brain Substantia Nigra	brain
43	chr3:136030600-136040200	Weak transcription	Pancreas	Pancrea
44	chr3:136031200-136038400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:136031800-136038200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:136032800-136055400	Weak transcription	HUVEC	blood vessel
47	chr3:136033400-136037400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:136034000-136038000	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:136034600-136038200	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:136034800-136038000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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