Variant report

Variant	rs1604068
Chromosome Location	chr3:46101684-46101685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46035149..46036764-chr3:46100668..46103208,2	K562	blood:
2	chr3:46095387..46098200-chr3:46100479..46102760,2	K562	blood:
3	chr3:46100682..46102669-chr3:46103976..46105710,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10510747	0.89[ASN][1000 genomes]
rs1118021	0.82[ASN][1000 genomes]
rs12486449	0.91[ASN][1000 genomes]
rs13320534	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs13434141	0.91[ASN][1000 genomes]
rs1388602	0.88[EUR][1000 genomes]
rs1392290	0.82[JPT][hapmap]
rs1491960	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.91[ASN][1000 genomes]
rs1546079	0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1602580	0.82[ASN][1000 genomes]
rs17078567	0.95[ASN][1000 genomes]
rs17078589	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036295	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173639	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2888512	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851347	0.82[JPT][hapmap]
rs4339141	0.85[ASN][1000 genomes]
rs4490402	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs4586860	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682804	0.89[ASN][1000 genomes]
rs4682805	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682807	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683169	0.91[ASN][1000 genomes]
rs4683174	0.98[ASN][1000 genomes]
rs56800498	0.90[ASN][1000 genomes]
rs58035200	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58260031	0.82[ASN][1000 genomes]
rs59865404	0.89[ASN][1000 genomes]
rs60991632	0.91[ASN][1000 genomes]
rs61066315	0.85[ASN][1000 genomes]
rs61387489	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62242846	0.99[ASN][1000 genomes]
rs62243869	0.98[ASN][1000 genomes]
rs62243873	0.89[ASN][1000 genomes]
rs6764042	0.82[JPT][hapmap]
rs6766515	0.81[AFR][1000 genomes]
rs6778958	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6780163	0.82[JPT][hapmap]
rs751625	0.89[ASN][1000 genomes]
rs7623460	0.82[JPT][hapmap]
rs7623476	0.86[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7641151	0.86[ASN][1000 genomes]
rs7641164	0.86[ASN][1000 genomes]
rs880160	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9818635	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9849715	0.86[ASN][1000 genomes]
rs9856805	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9990060	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1604068	CCDC12	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46096400-46106200	Weak transcription	Lung	lung
2	chr3:46099000-46105400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:46100600-46102600	Weak transcription	Right Atrium	heart
4	chr3:46100800-46102600	Weak transcription	Adipose Nuclei	Adipose
5	chr3:46100800-46103600	Weak transcription	Spleen	Spleen
6	chr3:46101000-46106400	Weak transcription	Primary B cells from cord blood	blood
7	chr3:46101200-46102400	Enhancers	GM12878-XiMat	blood
8	chr3:46101200-46104200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:46101400-46101800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr3:46101600-46102000	Enhancers	Fetal Heart	heart
11	chr3:46101600-46102400	Enhancers	Psoas Muscle	Psoas
12	chr3:46101600-46107000	Enhancers	Skeletal Muscle Female	skeletal muscle

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