Variant report

Variant	rs589092
Chromosome Location	chr3:135979698-135979699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135914058..135916023-chr3:135977800..135980119,2	MCF-7	breast:
2	chr3:135967759..135969790-chr3:135979580..135981663,2	K562	blood:
3	chr3:135967759..135970710-chr3:135979580..135983206,3	K562	blood:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction
ENSG00000114054	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10935177	0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10935182	0.89[ASW][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap]
rs10935183	0.92[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap]
rs10935184	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1145106	0.93[JPT][hapmap]
rs1153877	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];0.96[ASN][1000 genomes]
rs1154988	0.86[JPT][hapmap]
rs11717954	0.89[ASW][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap]
rs12488721	0.90[ASN][1000 genomes]
rs12492510	0.89[ASW][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap]
rs1278493	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs1279086	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1279424	0.87[ASN][1000 genomes]
rs1279425	1.00[JPT][hapmap]
rs1279831	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs1279840	1.00[JPT][hapmap]
rs1279949	0.96[ASN][1000 genomes]
rs1711161	0.87[JPT][hapmap]
rs1711170	0.86[JPT][hapmap]
rs1711171	1.00[JPT][hapmap]
rs2655008	0.93[JPT][hapmap]
rs3755636	1.00[JPT][hapmap]
rs3957816	0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4678428	1.00[JPT][hapmap]
rs480330	0.85[ASN][1000 genomes]
rs483465	1.00[JPT][hapmap]
rs518972	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]
rs521746	0.89[ASW][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs527888	0.87[ASN][1000 genomes]
rs548288	1.00[JPT][hapmap]
rs553018	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs556788	0.89[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs570621	0.96[ASN][1000 genomes]
rs571513	1.00[JPT][hapmap]
rs576771	0.93[JPT][hapmap]
rs590198	0.85[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]
rs632251	0.85[ASN][1000 genomes]
rs634559	0.85[ASN][1000 genomes]
rs645040	0.86[JPT][hapmap]
rs650326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs654237	0.89[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs655836	0.89[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs661739	0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs664088	0.84[ASN][1000 genomes]
rs667920	1.00[JPT][hapmap]
rs668437	0.83[ASN][1000 genomes]
rs6791611	0.92[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap]
rs684195	0.98[ASN][1000 genomes]
rs684773	0.86[JPT][hapmap]
rs687339	0.86[JPT][hapmap]
rs695983	0.93[JPT][hapmap]
rs696081	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs696516	0.93[JPT][hapmap]
rs696518	0.89[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap]
rs696520	0.89[ASW][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs698270	0.93[JPT][hapmap]
rs7372313	0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs7620314	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs834304	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs838202	0.87[ASN][1000 genomes]
rs864437	0.89[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap]
rs866758	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs895894	0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9810089	0.82[CHB][hapmap]
rs9811753	0.92[CHB][hapmap];1.00[YRI][hapmap]
rs9840812	0.86[JPT][hapmap]
rs9845457	0.83[CHB][hapmap];0.86[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	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	nsv933522	chr3:135968919-135981180	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
4	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs589092	PCCB	cis	lymphoblastoid	seeQTL
rs589092	SPSB4	cis	cerebellum	SCAN
rs589092	PCCB	cis	cerebellum	SCAN
rs589092	PCCB	cis	multi-tissue	Pritchard
rs589092	PCCB	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970000-135980000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:135970200-135980400	Weak transcription	Gastric	stomach
3	chr3:135970200-135984000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:135970200-135996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:135970400-135981600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:135970400-135995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:135970600-135985200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:135970600-135985200	Weak transcription	HMEC	breast
9	chr3:135970600-135987600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:135970600-135998800	Weak transcription	Fetal Brain Male	brain
11	chr3:135970600-135999200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:135970600-135999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:135970800-135981200	Weak transcription	Fetal Heart	heart
15	chr3:135970800-135986000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:135970800-135995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:135970800-135998000	Weak transcription	Hela-S3	cervix
18	chr3:135973400-135984200	Strong transcription	Fetal Stomach	stomach
19	chr3:135974000-135983400	Strong transcription	Fetal Thymus	thymus
20	chr3:135974000-135986800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:135974000-135986800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:135974000-135989400	Strong transcription	Dnd41	blood
23	chr3:135974200-135982400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:135974200-135982800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:135974200-135983200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:135974200-135983400	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:135974200-135989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:135974200-135989600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:135974400-135982600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:135974400-135983000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:135974400-135983000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:135974400-135983200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:135974400-135983600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:135974400-135984600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:135974400-135984600	Strong transcription	Liver	Liver
36	chr3:135974400-135986400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:135974400-135989600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:135974600-135981600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:135974600-135981800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:135974600-135982400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:135974600-135982800	Strong transcription	Left Ventricle	heart
42	chr3:135974600-135983000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:135974600-135983400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:135974600-135985200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr3:135974600-135986400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:135974800-135982800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:135974800-135983400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:135974800-135986200	Strong transcription	Placenta	Placenta
49	chr3:135974800-135997800	Weak transcription	Stomach Mucosa	stomach
50	chr3:135975000-135981800	Strong transcription	Rectal Mucosa Donor 31	rectum

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