Variant report

Variant	rs654237
Chromosome Location	chr3:136068699-136068700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1070232	0.93[JPT][hapmap]
rs10935181	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10935182	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs10935183	0.92[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs10935184	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs1145106	0.87[JPT][hapmap]
rs1153877	1.00[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1154988	0.81[JPT][hapmap]
rs11715257	0.87[JPT][hapmap]
rs11717954	1.00[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11915629	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12492510	1.00[ASW][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs1279086	0.82[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1279424	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1279425	0.93[JPT][hapmap]
rs1279831	0.80[JPT][hapmap];0.87[MEX][hapmap]
rs1279840	0.93[JPT][hapmap]
rs1279949	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1394092	0.93[JPT][hapmap]
rs1711161	0.81[JPT][hapmap]
rs1711170	0.81[JPT][hapmap]
rs1711171	0.93[JPT][hapmap]
rs2655008	0.87[JPT][hapmap]
rs3755636	0.93[JPT][hapmap]
rs3957816	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs4678428	0.93[JPT][hapmap]
rs4678433	0.93[JPT][hapmap]
rs480162	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480330	0.81[ASN][1000 genomes]
rs483465	0.93[JPT][hapmap]
rs517319	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs518972	1.00[ASW][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs521746	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs527888	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs548288	0.93[JPT][hapmap]
rs553018	0.83[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs556788	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]
rs56235965	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs570621	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs571513	0.93[JPT][hapmap]
rs576771	0.87[JPT][hapmap]
rs589092	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]
rs595532	0.83[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs606725	0.93[JPT][hapmap]
rs619605	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs645040	0.81[JPT][hapmap]
rs650326	0.83[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs655836	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs661739	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs664088	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66691851	0.81[EUR][1000 genomes]
rs667920	0.93[JPT][hapmap]
rs6791611	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs681783	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs684195	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs684773	0.81[JPT][hapmap]
rs687339	0.81[JPT][hapmap]
rs695983	0.87[JPT][hapmap]
rs696081	0.83[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs696516	0.87[JPT][hapmap]
rs696518	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs696520	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698269	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs698270	0.87[JPT][hapmap]
rs699165	0.93[JPT][hapmap]
rs711972	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs711975	1.00[ASW][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap]
rs73222302	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7372313	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs7620314	0.92[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs833752	0.93[JPT][hapmap]
rs834304	0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs834305	0.84[ASN][1000 genomes]
rs838202	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs864437	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs866758	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs895894	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs900048	0.87[JPT][hapmap]
rs9845457	0.81[JPT][hapmap]
rs9854084	0.93[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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs654237	PCCB	cis	multi-tissue	Pritchard
rs654237	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs654237	PCCB	cis	lymphoblastoid	seeQTL
rs654237	PCCB	cis	cerebellum	SCAN
rs654237	PCCB	cis	parietal	SCAN
rs654237	DBR1	cis	cerebellum	SCAN
rs654237	SPSB4	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136039000-136072400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:136042400-136078800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:136042600-136072600	Strong transcription	Dnd41	blood
4	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
5	chr3:136043600-136082000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:136043800-136070400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:136045600-136079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:136047600-136098000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:136047800-136074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:136051000-136069800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:136051600-136069200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:136051600-136070800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:136052200-136069200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:136052800-136070800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:136053000-136072400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:136053800-136069000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:136054200-136085400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:136054600-136074200	Weak transcription	Brain Angular Gyrus	brain
19	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:136054800-136076600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:136055400-136069000	Weak transcription	Aorta	Aorta
22	chr3:136055600-136073400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:136055600-136100800	Weak transcription	Spleen	Spleen
24	chr3:136057800-136069800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:136059000-136072000	Weak transcription	GM12878-XiMat	blood
26	chr3:136059200-136069200	Weak transcription	Psoas Muscle	Psoas
27	chr3:136059600-136070400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:136059600-136079000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:136060400-136069200	Weak transcription	Right Ventricle	heart
30	chr3:136061800-136074200	Weak transcription	Brain Germinal Matrix	brain
31	chr3:136063200-136071000	Weak transcription	Fetal Brain Female	brain
32	chr3:136063200-136072200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:136063400-136068800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:136063400-136069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:136063400-136069000	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:136063400-136069000	Weak transcription	Fetal Heart	heart
37	chr3:136063400-136069000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:136063400-136069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:136063400-136069000	Weak transcription	Thymus	Thymus
40	chr3:136063400-136069200	Weak transcription	Esophagus	oesophagus
41	chr3:136063400-136069200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:136063400-136069200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:136063400-136071800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:136063400-136072200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:136063400-136072200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:136063400-136073800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:136063600-136068800	Weak transcription	Left Ventricle	heart
50	chr3:136063600-136068800	Weak transcription	HMEC	breast

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