Variant report

Variant	rs641760
Chromosome Location	chr12:123518866-123518867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1051431	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs10846486	0.94[CEU][hapmap]
rs11057192	0.89[CEU][hapmap];0.97[TSI][hapmap]
rs1106240	0.94[CEU][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs1106241	0.94[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1260294	1.00[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs12811109	0.88[EUR][1000 genomes]
rs12820906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12828755	0.87[EUR][1000 genomes]
rs1402274	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1463877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1569068	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1615350	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1617156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1716157	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1716160	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716164	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1716165	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716167	0.94[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1716168	0.94[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1716170	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs1716171	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs1716175	0.94[CEU][hapmap]
rs1716176	0.94[CEU][hapmap]
rs1716177	0.94[CEU][hapmap]
rs1727294	0.93[CEU][hapmap];0.90[ASN][1000 genomes]
rs1727296	0.94[CEU][hapmap]
rs1727302	0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs1727306	0.94[CEU][hapmap]
rs1727309	0.94[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs1727313	0.94[CEU][hapmap];0.94[TSI][hapmap]
rs1727315	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1727320	0.94[CEU][hapmap]
rs1727323	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1727324	0.94[CEU][hapmap]
rs1727325	0.94[CEU][hapmap]
rs1727334	0.86[CEU][hapmap]
rs1790095	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1790098	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1790100	0.94[CEU][hapmap]
rs1790108	0.94[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1790116	0.88[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap]
rs1790120	0.85[ASN][1000 genomes]
rs1790123	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs1790131	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs2049114	0.94[CEU][hapmap]
rs2270789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2510885	0.90[ASN][1000 genomes]
rs2682434	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs2695478	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs2695482	0.94[CEU][hapmap]
rs2851447	0.82[CEU][hapmap]
rs4148856	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4372492	0.94[CEU][hapmap]
rs4460848	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs520088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs585522	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs655293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132277	0.94[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs71444568	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7296418	0.81[MEX][hapmap]
rs7299943	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[ASN][1000 genomes]
rs7975763	0.82[ASN][1000 genomes]
rs883263	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883563	0.86[EUR][1000 genomes]
rs884548	0.94[CEU][hapmap]
rs937564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs940904	0.93[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs941305	0.94[CEU][hapmap]
rs941306	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
8	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs641760	CDK2AP1	cis	lymphoblastoid	seeQTL
rs641760	HIP1R	cis	parietal	SCAN
rs641760	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs641760	PITPNM2	cis	cerebellum	SCAN
rs641760	WDR66	cis	parietal	SCAN
rs641760	ANAPC5	cis	parietal	SCAN
rs641760	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs641760	CCDC92	cis	cerebellum	SCAN
rs641760	MPHOSPH9	cis	Esophagus Muscularis	GTEx
rs641760	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs641760	TMEM120B	cis	parietal	SCAN
rs641760	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs641760	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs641760	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs641760	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
2	chr12:123490200-123528200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:123491600-123526400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:123496000-123526400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:123497400-123528600	Weak transcription	Ovary	ovary
6	chr12:123497800-123526000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:123502200-123519200	Weak transcription	HSMMtube	muscle
8	chr12:123504200-123519000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:123504200-123528000	Weak transcription	HMEC	breast
10	chr12:123504400-123540200	Weak transcription	Hela-S3	cervix
11	chr12:123507400-123526000	Genic enhancers	Fetal Thymus	thymus
12	chr12:123509800-123519000	Weak transcription	A549	lung
13	chr12:123509800-123519200	Weak transcription	HSMM	muscle
14	chr12:123509800-123519200	Weak transcription	Osteobl	bone
15	chr12:123509800-123525600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:123509800-123530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:123510200-123519600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:123510800-123519200	Strong transcription	Liver	Liver
19	chr12:123511000-123519400	Strong transcription	Fetal Stomach	stomach
20	chr12:123511400-123528200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:123514200-123519400	Strong transcription	Fetal Brain Female	brain
22	chr12:123515200-123519000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:123515400-123519200	Strong transcription	Fetal Intestine Small	intestine
24	chr12:123515600-123519200	Strong transcription	NHLF	lung
25	chr12:123515600-123521600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr12:123516000-123519000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:123516000-123519000	Strong transcription	Fetal Intestine Large	intestine
28	chr12:123516000-123519400	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr12:123516200-123519000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:123516400-123519000	Strong transcription	Colonic Mucosa	Colon
31	chr12:123516400-123519200	Strong transcription	Right Ventricle	heart
32	chr12:123516400-123527400	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:123516600-123519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:123516600-123527800	Weak transcription	Stomach Mucosa	stomach
35	chr12:123516800-123519400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:123517200-123521800	Enhancers	Primary hematopoietic stem cells	blood
37	chr12:123517400-123519000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:123517400-123519000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:123517400-123519200	Genic enhancers	Lung	lung
40	chr12:123517400-123520600	Enhancers	K562	blood
41	chr12:123517600-123519000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:123517600-123519000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:123517600-123519000	Strong transcription	Pancreas	Pancrea
44	chr12:123517600-123519200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:123517600-123519200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr12:123517600-123519800	Enhancers	Primary T cells fromperipheralblood	blood
47	chr12:123517800-123519000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:123517800-123519000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:123517800-123519000	Strong transcription	Gastric	stomach
50	chr12:123517800-123519000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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