Variant report

Variant	rs556788
Chromosome Location	chr3:136027549-136027550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136012746..136014476-chr3:136025907..136027620,2	K562	blood:
2	chr3:136010183..136011753-chr3:136025540..136027566,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10935177	0.85[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs10935181	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10935182	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs10935183	0.92[CEU][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs10935184	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1145106	0.93[JPT][hapmap]
rs1153877	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1154988	0.86[JPT][hapmap]
rs11715257	0.93[JPT][hapmap]
rs11717954	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes]
rs11915629	0.82[EUR][1000 genomes]
rs12488721	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12492510	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs1279086	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1279424	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1279425	1.00[JPT][hapmap]
rs1279831	0.85[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs1279840	1.00[JPT][hapmap]
rs1279949	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1394092	1.00[JPT][hapmap]
rs1711161	0.87[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	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs4678428	1.00[JPT][hapmap]
rs480162	0.91[AMR][1000 genomes];0.90[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	0.86[AMR][1000 genomes]
rs518972	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]
rs521746	1.00[ASW][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs527888	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548288	1.00[JPT][hapmap]
rs553018	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]
rs56235965	0.83[EUR][1000 genomes]
rs570621	0.93[AMR][1000 genomes];0.95[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];0.93[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];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs645040	0.86[JPT][hapmap]
rs650326	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654237	1.00[ASW][hapmap];0.82[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs655836	1.00[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs661739	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs664088	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66691851	0.84[EUR][1000 genomes]
rs667920	1.00[JPT][hapmap]
rs6791611	0.82[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs681783	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs684195	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs684773	0.86[JPT][hapmap]
rs687339	0.86[JPT][hapmap]
rs695983	0.93[JPT][hapmap]
rs696081	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs696516	0.93[JPT][hapmap]
rs696518	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.80[ASN][1000 genomes]
rs696520	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698270	0.93[JPT][hapmap]
rs699165	1.00[JPT][hapmap]
rs711972	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73222302	0.84[EUR][1000 genomes]
rs7372313	0.85[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs7620314	0.92[CHB][hapmap]
rs834304	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs834305	0.81[ASN][1000 genomes]
rs838202	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs864437	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs866758	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs895894	0.86[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:16 , 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	esv3461178	chr3:136019062-136028160	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv591834	chr3:136020975-136027549	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv591835	chr3:136020975-136027640	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv511202	chr3:136020975-136027769	Strong transcription Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv591840	chr3:136021052-136027640	Strong transcription Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv1793248	chr3:136021052-136027769	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1821255	chr3:136021052-136027769	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv1837661	chr3:136021052-136027769	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1838229	chr3:136021052-136027769	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv1841602	chr3:136021052-136027769	ZNF genes & repeats Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv1801263	chr3:136021656-136027769	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv591849	chr3:136024692-136027549	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs556788	SPSB4	cis	cerebellum	SCAN
rs556788	PCCB	cis	parietal	SCAN
rs556788	PCCB	cis	lymphoblastoid	seeQTL
rs556788	PCCB	cis	cerebellum	SCAN
rs556788	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs556788	DBR1	cis	cerebellum	SCAN
rs556788	PCCB	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 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	chr3:136020400-136030200	Weak transcription	Pancreas	Pancrea
20	chr3:136020400-136038400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:136020400-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:136020400-136045200	Weak transcription	Colonic Mucosa	Colon
23	chr3:136020600-136035000	Weak transcription	Fetal Brain Female	brain
24	chr3:136020600-136035200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:136020600-136035600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:136020600-136035600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:136020600-136035600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:136020600-136035800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:136020600-136035800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:136020600-136035800	Weak transcription	Aorta	Aorta
31	chr3:136020600-136035800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:136020600-136036000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:136020600-136036200	Weak transcription	Lung	lung
34	chr3:136020600-136036400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:136020600-136038000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:136020600-136038200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:136020600-136045000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:136020600-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:136020800-136030200	Weak transcription	Fetal Intestine Large	intestine
40	chr3:136020800-136030200	Weak transcription	Left Ventricle	heart
41	chr3:136020800-136035000	Weak transcription	Adipose Nuclei	Adipose
42	chr3:136020800-136035600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:136020800-136035600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:136020800-136035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:136020800-136035600	Weak transcription	K562	blood
46	chr3:136020800-136035800	Weak transcription	Fetal Lung	lung
47	chr3:136020800-136035800	Weak transcription	Ovary	ovary
48	chr3:136020800-136036200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:136020800-136037400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:136020800-136040200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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