Variant report

Variant	rs10840632
Chromosome Location	chr12:122375460-122375461
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	chr12:122374906..122377528-chr12:122380651..122382178,2	K562	blood:
2	chr12:122368373..122372240-chr12:122375380..122377746,3	K562	blood:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10840630	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840637	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11043220	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11043223	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs11043225	1.00[ASN][1000 genomes]
rs11043233	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043242	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11043243	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11043244	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043246	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043251	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043278	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043280	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043288	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1154514	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612028	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615980	0.82[EUR][1000 genomes]
rs1169070	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169071	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833399	1.00[CHD][hapmap]
rs12369331	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809676	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817066	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12822775	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12823194	1.00[ASN][1000 genomes]
rs12824593	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825161	1.00[ASN][1000 genomes]
rs12827036	1.00[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap]
rs12827452	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1720033	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720037	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167067	1.00[ASN][1000 genomes]
rs34159444	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906460	1.00[ASN][1000 genomes]
rs35244551	0.80[AMR][1000 genomes]
rs3847694	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs3887885	0.82[EUR][1000 genomes]
rs66611928	0.84[AFR][1000 genomes]
rs66751701	1.00[ASN][1000 genomes]
rs7132055	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137218	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7309024	0.82[EUR][1000 genomes]
rs7313252	0.96[CEU][hapmap]
rs73217776	1.00[ASN][1000 genomes]
rs7954584	0.90[MEX][hapmap]
rs9739381	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10840632	CCDC60	cis	cerebellum	SCAN
rs10840632	WDR66	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122357000-122380400	Weak transcription	Gastric	stomach
2	chr12:122357000-122383600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:122363000-122384800	Weak transcription	Psoas Muscle	Psoas
4	chr12:122363000-122393400	Weak transcription	Brain Angular Gyrus	brain
5	chr12:122363200-122384600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:122363400-122377000	Weak transcription	Fetal Intestine Small	intestine
7	chr12:122363600-122377400	Weak transcription	Fetal Brain Female	brain
8	chr12:122363600-122383600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:122363600-122383800	Weak transcription	Fetal Brain Male	brain
10	chr12:122363600-122385600	Weak transcription	Fetal Lung	lung
11	chr12:122363600-122392200	Weak transcription	Left Ventricle	heart
12	chr12:122363600-122398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
14	chr12:122365600-122385800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:122365600-122393400	Weak transcription	Brain Substantia Nigra	brain
16	chr12:122365800-122390200	Weak transcription	HUVEC	blood vessel
17	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:122366000-122376800	Weak transcription	HMEC	breast
19	chr12:122369600-122375800	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:122369600-122376000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr12:122369600-122376000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:122369800-122376800	Weak transcription	Placenta	Placenta
23	chr12:122370600-122387800	Weak transcription	NHDF-Ad	bronchial
24	chr12:122370600-122403200	Weak transcription	Fetal Kidney	kidney
25	chr12:122372000-122375800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:122372000-122376000	Strong transcription	NHLF	lung
27	chr12:122372200-122379600	Weak transcription	NH-A	brain
28	chr12:122372200-122396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:122372400-122376200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:122372400-122377400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:122372400-122378600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:122372800-122393600	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:122373800-122376000	Strong transcription	Brain Anterior Caudate	brain
34	chr12:122374000-122376200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:122374000-122402800	Weak transcription	HSMM	muscle
36	chr12:122374000-122405600	Weak transcription	Adipose Nuclei	Adipose
37	chr12:122374400-122375600	Strong transcription	Pancreas	Pancrea
38	chr12:122374600-122376000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:122374800-122375800	Strong transcription	K562	blood
40	chr12:122374800-122376000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:122374800-122376000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:122374800-122382200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:122375000-122375800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:122375000-122375800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:122375000-122375800	Strong transcription	Liver	Liver
46	chr12:122375000-122375800	ZNF genes & repeats	Thymus	Thymus
47	chr12:122375000-122375800	Strong transcription	HSMMtube	muscle
48	chr12:122375000-122376000	Strong transcription	Aorta	Aorta
49	chr12:122375000-122376000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr12:122375000-122376000	Strong transcription	Osteobl	bone

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