Variant report

Variant	rs12486660
Chromosome Location	chr3:100024553-100024554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100019084..100021966-chr3:100023421..100025437,2	K562	blood:

Variant related genes	Relation type
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1060452	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11918291	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11920015	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11923373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11924911	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486865	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12490043	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12490140	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12492610	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12493917	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17335566	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17335614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2171205	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277657	0.88[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs4928116	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4928117	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4928120	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs4928161	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4928166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55950446	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181320	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56311459	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57271189	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62281663	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]

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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12486660	TBC1D23	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
2	chr3:99980600-100053200	Weak transcription	Gastric	stomach
3	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
4	chr3:99986600-100024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:99989000-100025000	Weak transcription	Fetal Brain Female	brain
6	chr3:99990600-100030600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:99994400-100040800	Weak transcription	Esophagus	oesophagus
8	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
10	chr3:99996400-100025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:99997800-100031800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:99998400-100028000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:99998600-100026400	Strong transcription	HSMM	muscle
14	chr3:99998600-100033800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:99998800-100026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:100007000-100045000	Weak transcription	Lung	lung
17	chr3:100007800-100035800	Weak transcription	A549	lung
18	chr3:100008400-100026800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:100008600-100053000	Weak transcription	Aorta	Aorta
20	chr3:100009000-100025400	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:100009200-100045000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:100009400-100031800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:100009600-100024600	Weak transcription	HUVEC	blood vessel
24	chr3:100011600-100025600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:100011800-100025200	Weak transcription	Right Ventricle	heart
26	chr3:100011800-100028400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:100013400-100027800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:100013600-100026600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:100013600-100028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:100013800-100028200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:100014400-100030000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:100014600-100042200	Weak transcription	Fetal Brain Male	brain
33	chr3:100014800-100025200	Weak transcription	GM12878-XiMat	blood
34	chr3:100014800-100029400	Strong transcription	Liver	Liver
35	chr3:100015400-100053200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:100017000-100029800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:100017200-100025400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:100017200-100028600	Strong transcription	NHDF-Ad	bronchial
39	chr3:100017400-100025000	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:100017600-100025200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:100017600-100025200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:100018200-100025000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr3:100018200-100028800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:100018400-100024800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:100018400-100025600	Strong transcription	Adipose Nuclei	Adipose
46	chr3:100018400-100028000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:100018800-100025200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:100018800-100035800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:100019000-100024800	Weak transcription	Brain Germinal Matrix	brain
50	chr3:100019000-100043200	Weak transcription	Brain Angular Gyrus	brain

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