Variant report

Variant	rs527888
Chromosome Location	chr3:136031358-136031359
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136029722..136031537-chr3:136047190..136050098,2	MCF-7	breast:
2	chr3:135914356..135915920-chr3:136030171..136032687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

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[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10935182	0.81[EUR][1000 genomes]
rs10935184	0.90[EUR][1000 genomes]
rs1153877	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11717954	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11915629	0.84[EUR][1000 genomes]
rs12488721	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1279086	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1279424	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1279949	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1711170	0.81[ASN][1000 genomes]
rs480162	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs480330	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs517319	0.86[AMR][1000 genomes]
rs518972	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553018	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556788	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56235965	0.84[EUR][1000 genomes]
rs570621	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs589092	0.87[ASN][1000 genomes]
rs619605	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs650326	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654237	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs655836	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs664088	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66691851	0.86[EUR][1000 genomes]
rs6791611	0.83[EUR][1000 genomes]
rs681783	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs684195	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs696081	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs696518	0.80[ASN][1000 genomes]
rs696520	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs711972	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73222302	0.85[EUR][1000 genomes]
rs834304	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs834305	0.81[ASN][1000 genomes]
rs838202	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs866758	0.81[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs527888	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs527888	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 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	chr3:136010600-136031400	Weak transcription	Stomach Mucosa	stomach
8	chr3:136014200-136040000	Weak transcription	Small Intestine	intestine
9	chr3:136015000-136038800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:136016400-136038400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:136016800-136045600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:136017000-136040000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:136018200-136051400	Weak transcription	A549	lung
14	chr3:136019000-136038600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:136020200-136036400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:136020200-136039000	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:136020200-136040200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:136020200-136045200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:136020400-136038400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:136020400-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:136020400-136045200	Weak transcription	Colonic Mucosa	Colon
22	chr3:136020600-136035000	Weak transcription	Fetal Brain Female	brain
23	chr3:136020600-136035200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:136020600-136035600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:136020600-136035600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:136020600-136035600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:136020600-136035800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:136020600-136035800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:136020600-136035800	Weak transcription	Aorta	Aorta
30	chr3:136020600-136035800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:136020600-136036000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:136020600-136036200	Weak transcription	Lung	lung
33	chr3:136020600-136036400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:136020600-136038000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:136020600-136038200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:136020600-136045000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:136020600-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:136020800-136035000	Weak transcription	Adipose Nuclei	Adipose
39	chr3:136020800-136035600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:136020800-136035600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr3:136020800-136035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:136020800-136035600	Weak transcription	K562	blood
43	chr3:136020800-136035800	Weak transcription	Fetal Lung	lung
44	chr3:136020800-136035800	Weak transcription	Ovary	ovary
45	chr3:136020800-136036200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:136020800-136037400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:136020800-136040200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:136020800-136040200	Weak transcription	Esophagus	oesophagus
49	chr3:136020800-136042200	Weak transcription	Placenta	Placenta
50	chr3:136020800-136043000	Weak transcription	HSMM	muscle

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