Variant report

Variant	rs571513
Chromosome Location	chr3:136095035-136095036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1070232	1.00[JPT][hapmap]
rs10935182	0.93[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs1145101	0.89[MEX][hapmap]
rs1145106	0.92[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1153877	1.00[JPT][hapmap]
rs1154988	0.86[JPT][hapmap]
rs11715257	0.94[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[ASN][1000 genomes]
rs11717954	0.87[JPT][hapmap]
rs12330635	0.89[CHB][hapmap]
rs12492510	0.87[JPT][hapmap]
rs12637102	0.88[EUR][1000 genomes]
rs1279086	1.00[JPT][hapmap]
rs1279425	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1279831	0.86[JPT][hapmap]
rs1279840	0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs1291921	0.84[ASN][1000 genomes]
rs13068119	0.94[MEX][hapmap]
rs1394092	1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs1618069	0.85[ASN][1000 genomes]
rs1711161	0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1711170	0.86[JPT][hapmap]
rs1711171	0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs17252498	0.83[MEX][hapmap]
rs1964675	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2655008	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28478252	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34967300	0.94[MEX][hapmap]
rs3755636	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3821445	0.89[MEX][hapmap]
rs3957816	0.86[JPT][hapmap]
rs4678428	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs4678433	1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs483465	1.00[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs518972	1.00[JPT][hapmap]
rs521746	0.87[JPT][hapmap]
rs548288	0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs553018	0.93[JPT][hapmap]
rs556788	1.00[JPT][hapmap]
rs576771	0.87[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs589092	1.00[JPT][hapmap]
rs595532	0.93[JPT][hapmap]
rs606725	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs619605	0.93[JPT][hapmap]
rs645040	0.86[JPT][hapmap]
rs650326	1.00[JPT][hapmap]
rs654237	0.93[JPT][hapmap]
rs655720	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs655836	0.93[JPT][hapmap]
rs661739	0.86[JPT][hapmap]
rs667920	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6770476	0.81[ASN][1000 genomes]
rs6789488	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6791611	0.87[JPT][hapmap]
rs6794351	0.90[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs684773	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs687339	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs695983	1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs696081	1.00[JPT][hapmap]
rs696516	0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.94[ASN][1000 genomes]
rs696517	0.84[ASW][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap]
rs696518	0.93[JPT][hapmap]
rs696520	1.00[JPT][hapmap]
rs698270	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs699165	0.94[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs711975	0.93[JPT][hapmap]
rs7432375	0.93[JPT][hapmap]
rs7621025	0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs7644541	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833752	0.89[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs895894	0.86[JPT][hapmap]
rs900048	1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs9289511	1.00[CHB][hapmap]
rs9809427	0.87[ASN][1000 genomes]
rs9820485	1.00[CHB][hapmap]
rs9832056	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs9832556	0.83[ASN][1000 genomes]
rs9832813	1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs9845457	0.86[JPT][hapmap]
rs9848883	0.89[CHB][hapmap]
rs9851986	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs9854084	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9856769	0.89[CHB][hapmap]
rs9869720	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs9883916	0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers 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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs571513	PCCB	cis	lymphoblastoid	seeQTL
rs571513	NCK1	cis	parietal	SCAN
rs571513	MSL2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
2	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:136055600-136100800	Weak transcription	Spleen	Spleen
5	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:136063600-136097000	Weak transcription	Colonic Mucosa	Colon
8	chr3:136063600-136105600	Weak transcription	Gastric	stomach
9	chr3:136063600-136110600	Weak transcription	Small Intestine	intestine
10	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
11	chr3:136063800-136095200	Weak transcription	Lung	lung
12	chr3:136065400-136097200	Weak transcription	HepG2	liver
13	chr3:136067600-136109000	Weak transcription	HUVEC	blood vessel
14	chr3:136068600-136103800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:136069400-136121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:136069600-136107400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:136069600-136138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:136069600-136139400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:136069800-136106600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:136069800-136118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:136070600-136101000	Weak transcription	Right Ventricle	heart
23	chr3:136070600-136105800	Weak transcription	Psoas Muscle	Psoas
24	chr3:136070800-136095200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:136070800-136096800	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:136070800-136096800	Weak transcription	HSMMtube	muscle
27	chr3:136070800-136099600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:136070800-136112200	Weak transcription	Aorta	Aorta
29	chr3:136070800-136121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:136072600-136098800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:136072800-136097000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:136072800-136100400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:136075000-136137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:136075400-136108000	Weak transcription	Fetal Brain Female	brain
35	chr3:136075600-136097000	Weak transcription	Fetal Lung	lung
36	chr3:136075600-136105800	Weak transcription	Ovary	ovary
37	chr3:136075800-136099000	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
39	chr3:136078200-136096000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:136081200-136118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:136081400-136095200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:136083200-136111400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:136084400-136123200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:136085400-136104200	Weak transcription	GM12878-XiMat	blood
46	chr3:136085600-136095200	Weak transcription	Adipose Nuclei	Adipose
47	chr3:136085600-136100000	Weak transcription	Osteobl	bone
48	chr3:136085600-136116400	Weak transcription	Fetal Intestine Large	intestine
49	chr3:136085800-136095200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:136085800-136099400	Weak transcription	Muscle Satellite Cultured Cells	--

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