Variant report

Variant	rs4683367
Chromosome Location	chr3:43257827-43257828
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43233608..43236021-chr3:43256055..43258322,2	MCF-7	breast:
2	chr3:43235922..43238512-chr3:43256089..43258366,2	K562	blood:
3	chr3:43254448..43258211-chr3:43258239..43261327,4	K562	blood:
4	chr3:43257334..43257885-chr3:43419375..43420223,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10865932	0.88[GIH][hapmap];0.93[TSI][hapmap]
rs11129996	0.94[ASN][1000 genomes]
rs12634274	0.81[GIH][hapmap]
rs12715387	0.95[ASN][1000 genomes]
rs12715388	0.95[ASN][1000 genomes]
rs13059783	0.95[ASN][1000 genomes]
rs13060695	0.95[ASN][1000 genomes]
rs13066699	0.95[ASN][1000 genomes]
rs13074235	0.91[ASN][1000 genomes]
rs13085652	0.95[ASN][1000 genomes]
rs1316296	0.98[EUR][1000 genomes]
rs1316297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1320156	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1320158	0.95[ASN][1000 genomes]
rs13320571	0.88[GIH][hapmap];0.93[TSI][hapmap]
rs1573931	0.94[ASN][1000 genomes]
rs1588027	0.82[GIH][hapmap]
rs17075317	0.92[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs17075335	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17075342	0.98[EUR][1000 genomes]
rs17075378	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17075381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17075398	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075597	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs1814902	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2372352	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2372354	0.92[ASN][1000 genomes]
rs2372355	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2372356	0.95[ASN][1000 genomes]
rs2888295	0.95[ASN][1000 genomes]
rs2888296	0.95[ASN][1000 genomes]
rs4016130	1.00[ASN][1000 genomes]
rs4260403	0.94[ASN][1000 genomes]
rs4404425	0.95[ASN][1000 genomes]
rs4419357	0.90[ASN][1000 genomes]
rs4444688	0.95[ASN][1000 genomes]
rs4585168	0.98[EUR][1000 genomes]
rs4637262	0.95[ASN][1000 genomes]
rs4682675	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682677	0.81[EUR][1000 genomes]
rs4682685	0.82[GIH][hapmap]
rs4682872	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682874	0.90[EUR][1000 genomes]
rs4682875	0.91[EUR][1000 genomes]
rs4682876	0.89[EUR][1000 genomes]
rs4682879	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683363	0.98[ASN][1000 genomes]
rs4683364	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4683366	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4683369	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442144	0.98[ASN][1000 genomes]
rs6762503	0.97[ASN][1000 genomes]
rs6781696	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6783741	0.82[GIH][hapmap]
rs6798619	0.91[ASN][1000 genomes]
rs6800983	0.82[GIH][hapmap]
rs6803929	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs6805075	0.95[ASN][1000 genomes]
rs7611123	0.98[EUR][1000 genomes]
rs7621298	0.85[JPT][hapmap]
rs7621511	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627198	0.95[ASN][1000 genomes]
rs7636673	1.00[ASN][1000 genomes]
rs7639584	0.97[ASN][1000 genomes]
rs7639605	1.00[ASN][1000 genomes]
rs9311334	0.98[ASN][1000 genomes]
rs9311335	0.95[ASN][1000 genomes]
rs9311336	0.95[ASN][1000 genomes]
rs9311339	0.82[GIH][hapmap]
rs9681394	0.85[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs9683242	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs977911	0.82[GIH][hapmap]
rs9809273	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9820946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9822961	0.97[ASN][1000 genomes]
rs9826102	0.95[ASN][1000 genomes]
rs9826849	0.95[ASN][1000 genomes]
rs9827911	0.95[ASN][1000 genomes]
rs9833793	1.00[ASN][1000 genomes]
rs9852399	0.94[ASN][1000 genomes]
rs9853795	0.98[ASN][1000 genomes]
rs9858012	1.00[CHB][hapmap];0.84[JPT][hapmap];0.98[ASN][1000 genomes]
rs9860007	0.95[ASN][1000 genomes]
rs9860364	0.97[ASN][1000 genomes]
rs9861337	0.97[ASN][1000 genomes]
rs9861529	0.97[ASN][1000 genomes]
rs9875582	0.85[CHB][hapmap];0.95[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3439212	chr3:43257514-43258236	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
3	esv3413981	chr3:43257522-43258240	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4683367	SPAG6	trans	brain	seeQTL
rs4683367	TEKT1	trans	brain	seeQTL
rs4683367	CAPS	trans	brain	seeQTL
rs4683367	CAPSL	trans	brain	seeQTL
rs4683367	SLC47A2	trans	brain	seeQTL
rs4683367	IQCG	trans	brain	seeQTL
rs4683367	FANK1	trans	brain	seeQTL
rs4683367	C1orf194	trans	brain	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43245000-43258800	Weak transcription	Right Atrium	heart
2	chr3:43247800-43259000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:43253200-43262400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:43253400-43259000	Weak transcription	Spleen	Spleen
5	chr3:43254000-43258000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:43256200-43266800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:43256200-43267000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:43256600-43260600	Weak transcription	Fetal Kidney	kidney
9	chr3:43256600-43264000	Enhancers	Primary T cells from cord blood	blood
10	chr3:43256800-43261000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:43256800-43264800	Enhancers	Fetal Thymus	thymus
12	chr3:43256800-43264800	Enhancers	Thymus	Thymus
13	chr3:43257000-43260400	Enhancers	NHEK	skin
14	chr3:43257000-43262400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:43257200-43260400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:43257200-43260400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:43257200-43260600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr3:43257200-43269400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:43257400-43266600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:43257600-43258200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:43257800-43258600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:43257800-43259000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:43257800-43260000	Weak transcription	Left Ventricle	heart
24	chr3:43257800-43262600	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links