Variant report

Variant	rs483465
Chromosome Location	chr3:136047977-136047978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135913060..135914977-chr3:136047197..136049788,2	K562	blood:
2	chr3:136029722..136031537-chr3:136047190..136050098,2	MCF-7	breast:
3	chr3:135910806..135913701-chr3:136047268..136049984,2	MCF-7	breast:
4	chr3:136043746..136046467-chr3:136047031..136048993,2	K562	blood:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10935177	0.86[JPT][hapmap]
rs10935182	0.93[JPT][hapmap]
rs10935183	0.87[JPT][hapmap]
rs10935184	1.00[JPT][hapmap]
rs1145101	0.94[MEX][hapmap]
rs1145106	0.92[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1153877	1.00[JPT][hapmap]
rs1154988	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs11715257	0.91[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs11717954	0.87[JPT][hapmap]
rs12330635	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12492510	0.87[JPT][hapmap]
rs1279086	1.00[JPT][hapmap]
rs1279425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1279831	0.86[JPT][hapmap]
rs1279840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1291921	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13068119	0.88[MEX][hapmap]
rs1394092	0.90[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs1618069	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1711161	0.90[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1711170	0.86[JPT][hapmap]
rs1711171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252498	0.88[MEX][hapmap]
rs1964675	0.85[AFR][1000 genomes]
rs2655008	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs28478252	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3755636	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3821445	0.84[CEU][hapmap];0.94[MEX][hapmap]
rs3957816	0.86[JPT][hapmap]
rs4678428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs518972	1.00[JPT][hapmap]
rs521746	0.87[JPT][hapmap]
rs548288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs553018	0.93[JPT][hapmap]
rs556788	1.00[JPT][hapmap]
rs571513	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]
rs576771	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs589092	1.00[JPT][hapmap]
rs595532	0.93[JPT][hapmap]
rs606725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610860	0.84[CEU][hapmap]
rs619605	0.93[JPT][hapmap]
rs632016	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs645040	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs650326	1.00[JPT][hapmap]
rs650505	0.93[ASN][1000 genomes]
rs654237	0.93[JPT][hapmap]
rs655720	0.85[ASN][1000 genomes]
rs655836	0.93[JPT][hapmap]
rs661739	0.86[JPT][hapmap]
rs665200	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667920	0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6770476	0.83[ASN][1000 genomes]
rs6789488	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6791611	0.87[JPT][hapmap]
rs684773	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs687339	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs695983	0.89[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs696081	1.00[JPT][hapmap]
rs696516	0.85[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs696517	0.84[ASW][hapmap];0.84[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes]
rs696518	0.93[JPT][hapmap]
rs696520	1.00[JPT][hapmap]
rs698270	1.00[ASW][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs699165	0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs711975	0.93[JPT][hapmap]
rs72493178	0.85[ASN][1000 genomes]
rs73222262	0.84[ASN][1000 genomes]
rs7372313	0.86[JPT][hapmap]
rs7628146	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8045	0.83[MEX][hapmap]
rs834304	0.85[JPT][hapmap]
rs864437	0.87[JPT][hapmap]
rs866758	0.87[JPT][hapmap]
rs895894	0.86[JPT][hapmap]
rs900048	0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs9820485	0.89[CHB][hapmap]
rs9832056	0.89[CHB][hapmap]
rs9832813	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs9845457	0.86[JPT][hapmap]
rs9848883	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs9851986	0.89[CHB][hapmap]
rs9854084	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9856769	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs9869720	0.89[CHB][hapmap]
rs9883916	0.88[MEX][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	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs483465	PCCB	cis	lymphoblastoid	seeQTL
rs483465	MSL2	cis	cerebellum	SCAN
rs483465	NCK1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135981200-136052000	Weak transcription	NH-A	brain
2	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
3	chr3:136018200-136051400	Weak transcription	A549	lung
4	chr3:136032800-136055400	Weak transcription	HUVEC	blood vessel
5	chr3:136039000-136072400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:136039200-136062400	Weak transcription	Fetal Heart	heart
7	chr3:136040200-136051200	Weak transcription	NHDF-Ad	bronchial
8	chr3:136040400-136062800	Weak transcription	Stomach Mucosa	stomach
9	chr3:136040600-136061400	Weak transcription	Small Intestine	intestine
10	chr3:136041000-136052800	Weak transcription	Fetal Kidney	kidney
11	chr3:136042000-136048800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:136042200-136048800	Strong transcription	Primary T cells from cord blood	blood
13	chr3:136042400-136058200	Weak transcription	Psoas Muscle	Psoas
14	chr3:136042400-136078800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:136042600-136053200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:136042600-136072600	Strong transcription	Dnd41	blood
17	chr3:136042800-136050000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:136043000-136048800	Strong transcription	Brain Anterior Caudate	brain
19	chr3:136043000-136048800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:136043200-136048800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:136043400-136048400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:136043400-136098600	Weak transcription	Fetal Brain Male	brain
23	chr3:136043600-136082000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:136043800-136048800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:136043800-136048800	Strong transcription	Fetal Intestine Small	intestine
26	chr3:136043800-136050200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:136043800-136070400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:136044200-136049000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:136044400-136050200	Strong transcription	Primary B cells from cord blood	blood
30	chr3:136044600-136048800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:136044800-136048800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:136044800-136048800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:136044800-136049000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:136044800-136049000	Strong transcription	Fetal Intestine Large	intestine
35	chr3:136044800-136054600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr3:136045000-136048400	Strong transcription	Placenta	Placenta
37	chr3:136045000-136048800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:136045000-136048800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:136045000-136048800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:136045000-136048800	Strong transcription	Brain Substantia Nigra	brain
41	chr3:136045000-136048800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:136045000-136048800	Strong transcription	Fetal Brain Female	brain
43	chr3:136045000-136048800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:136045000-136049000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:136045000-136049000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:136045000-136049000	Strong transcription	Brain Hippocampus Middle	brain
47	chr3:136045000-136049000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:136045000-136049200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:136045000-136049200	Strong transcription	HepG2	liver
50	chr3:136045000-136049400	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links