Variant report

Variant	rs2420512
Chromosome Location	chr1:169815072-169815073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169813665..169815297-chr1:169863390..169865357,2	K562	blood:
2	chr1:169811782..169814022-chr1:169814299..169816027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10733054	0.84[EUR][1000 genomes]
rs10737549	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10737550	0.95[ASN][1000 genomes]
rs10737551	0.92[ASN][1000 genomes]
rs10800479	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800480	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800481	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10800483	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800484	0.94[ASN][1000 genomes]
rs10800485	0.96[EUR][1000 genomes]
rs10800486	0.92[EUR][1000 genomes]
rs10919239	0.84[EUR][1000 genomes]
rs10919245	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919248	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919251	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10919257	0.95[ASN][1000 genomes]
rs10919263	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133843	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883436	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2056980	0.82[EUR][1000 genomes]
rs2056981	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179396	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2205851	0.84[EUR][1000 genomes]
rs2281039	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294322	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294496	0.95[ASN][1000 genomes]
rs2420514	0.92[EUR][1000 genomes]
rs2491087	0.88[EUR][1000 genomes]
rs2806386	0.86[EUR][1000 genomes]
rs2901179	0.89[ASN][1000 genomes]
rs3753308	0.93[EUR][1000 genomes]
rs3766132	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766137	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766142	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766144	0.94[ASN][1000 genomes]
rs3766148	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766151	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766154	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4376791	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508080	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4614317	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4615900	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656196	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656197	0.95[ASN][1000 genomes]
rs4656199	0.95[ASN][1000 genomes]
rs4656200	0.95[ASN][1000 genomes]
rs4656721	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656724	0.95[ASN][1000 genomes]
rs4656725	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427217	0.84[EUR][1000 genomes]
rs6427220	0.90[ASN][1000 genomes]
rs6427224	0.95[ASN][1000 genomes]
rs6427225	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6427226	0.89[ASN][1000 genomes]
rs6427227	0.90[ASN][1000 genomes]
rs6427228	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6656965	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664099	0.95[ASN][1000 genomes]
rs6668114	0.88[ASN][1000 genomes]
rs6669794	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6670818	0.93[EUR][1000 genomes]
rs6671752	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676810	0.84[EUR][1000 genomes]
rs6680508	0.84[EUR][1000 genomes]
rs6680650	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680938	0.87[ASN][1000 genomes]
rs6682137	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6682835	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6683056	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6684481	0.95[ASN][1000 genomes]
rs6687377	0.93[ASN][1000 genomes]
rs6702969	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs717481	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732185	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7519364	0.94[ASN][1000 genomes]
rs7525259	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526261	0.84[EUR][1000 genomes]
rs7530237	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545011	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9287097	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2420512	C1orf112	Cis_1M	lymphoblastoid	RTeQTL
rs2420512	SCYL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169818200	Weak transcription	Esophagus	oesophagus
2	chr1:169764800-169818200	Weak transcription	Lung	lung
3	chr1:169764800-169823600	Weak transcription	Gastric	stomach
4	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:169765200-169815200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:169765200-169818800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:169765200-169820600	Weak transcription	Psoas Muscle	Psoas
8	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
9	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
10	chr1:169765600-169818200	Weak transcription	NHLF	lung
11	chr1:169765800-169815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:169765800-169818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:169777400-169815400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:169786600-169841400	Strong transcription	Dnd41	blood
16	chr1:169788600-169823600	Weak transcription	Pancreas	Pancrea
17	chr1:169789200-169818600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
19	chr1:169793800-169822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:169794200-169818400	Weak transcription	NHEK	skin
21	chr1:169794800-169822000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:169797000-169818200	Weak transcription	Spleen	Spleen
23	chr1:169797600-169818200	Weak transcription	HSMMtube	muscle
24	chr1:169802200-169822600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:169802400-169821800	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:169802800-169819800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:169806400-169820600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
30	chr1:169807000-169816600	Weak transcription	NHDF-Ad	bronchial
31	chr1:169808000-169815200	Weak transcription	Fetal Stomach	stomach
32	chr1:169808200-169819800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:169808200-169822000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:169808200-169841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:169808400-169818200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:169808400-169818400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:169808600-169821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:169808600-169827000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:169808800-169815800	Weak transcription	Thymus	Thymus
40	chr1:169808800-169816200	Strong transcription	Adipose Nuclei	Adipose
41	chr1:169808800-169817800	Weak transcription	Fetal Brain Male	brain
42	chr1:169808800-169818200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:169808800-169818200	Weak transcription	Small Intestine	intestine
44	chr1:169808800-169818600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:169808800-169823200	Weak transcription	Fetal Heart	heart
46	chr1:169809200-169817800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:169809200-169829400	Strong transcription	GM12878-XiMat	blood
48	chr1:169809200-169829600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:169809400-169815400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:169809800-169816400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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