Variant report

Variant	rs12639142
Chromosome Location	chr3:42831532-42831533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42829524..42832702-chr3:42860935..42865948,4	MCF-7	breast:
2	chr3:42831182..42835559-chr3:42843260..42847112,5	K562	blood:
3	chr3:42830549..42834930-chr3:42834971..42839390,5	K562	blood:

Variant related genes	Relation type
ENSG00000181061	Chromatin interaction
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10490794	0.87[CHB][hapmap]
rs10865922	0.87[CHB][hapmap]
rs11129975	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11129976	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11129977	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11718476	0.86[CHB][hapmap]
rs11922251	0.87[CHB][hapmap]
rs11922832	0.96[CEU][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11929390	0.87[CHB][hapmap]
rs12491179	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12635736	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs13070029	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13070345	0.87[CHB][hapmap]
rs13096498	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2240859	0.87[CHB][hapmap]
rs2372110	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339671	0.89[EUR][1000 genomes]
rs339684	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs339731	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34868846	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35584330	0.88[EUR][1000 genomes]
rs3843369	0.90[EUR][1000 genomes]
rs3846063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3895740	0.87[CHB][hapmap]
rs3907218	0.87[CHB][hapmap]
rs3912104	0.87[CHB][hapmap]
rs4683332	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4683335	0.95[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs6442067	0.92[EUR][1000 genomes]
rs6779561	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs7639170	0.87[CHB][hapmap]
rs7639483	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs7641046	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9830553	0.86[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12639142	CCDC13	cis	cerebellum	SCAN
rs12639142	CCDC13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42814800-42840800	Weak transcription	Spleen	Spleen
2	chr3:42815000-42834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:42815200-42834800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:42815200-42834800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:42815200-42834800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:42815200-42834800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:42815200-42834800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:42815200-42834800	Weak transcription	Ovary	ovary
9	chr3:42815200-42834800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:42815200-42834800	Weak transcription	A549	lung
11	chr3:42815200-42835200	Weak transcription	Right Ventricle	heart
12	chr3:42815200-42836400	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:42815200-42837400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:42815200-42842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:42815200-42842200	Weak transcription	Aorta	Aorta
16	chr3:42815200-42842400	Weak transcription	Psoas Muscle	Psoas
17	chr3:42815400-42832400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:42815400-42833600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:42815400-42834400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:42815400-42834800	Weak transcription	Brain Germinal Matrix	brain
21	chr3:42815400-42837200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:42815400-42844000	Weak transcription	NHDF-Ad	bronchial
23	chr3:42815600-42841800	Weak transcription	Thymus	Thymus
24	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:42816200-42837600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:42820400-42834800	Weak transcription	HSMMtube	muscle
28	chr3:42821400-42837400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:42821800-42834800	Weak transcription	Esophagus	oesophagus
30	chr3:42821800-42834800	Weak transcription	Pancreas	Pancrea
31	chr3:42822000-42841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:42822400-42834800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:42822400-42834800	Weak transcription	NHLF	lung
34	chr3:42822400-42837200	Weak transcription	Brain Angular Gyrus	brain
35	chr3:42822400-42843400	Weak transcription	Small Intestine	intestine
36	chr3:42822800-42834800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:42822800-42837000	Weak transcription	Brain Anterior Caudate	brain
38	chr3:42822800-42841600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:42822800-42842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:42822800-42844000	Weak transcription	Fetal Kidney	kidney
41	chr3:42822800-42844200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:42823000-42832400	Weak transcription	Fetal Heart	heart
43	chr3:42823000-42842800	Weak transcription	Fetal Brain Male	brain
44	chr3:42823600-42834800	Weak transcription	Colonic Mucosa	Colon
45	chr3:42823600-42836400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:42824000-42835400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:42824000-42836400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:42824400-42836400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:42825000-42834800	Weak transcription	Fetal Brain Female	brain
50	chr3:42825200-42834800	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links