Variant report

Variant	rs12023668
Chromosome Location	chr1:57169425-57169426
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	chr1:55923553..55925423-chr1:57168281..57171195,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10749708	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10789036	0.85[ASN][1000 genomes]
rs10789038	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10789040	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10789041	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889006	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10889008	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10889009	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11206884	0.88[ASN][1000 genomes]
rs11206885	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11206886	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11206888	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11206889	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11206890	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11206895	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11589368	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804779	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12021768	0.88[ASN][1000 genomes]
rs12021851	0.88[ASN][1000 genomes]
rs12032999	0.86[ASN][1000 genomes]
rs12048572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073311	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12078260	0.85[ASN][1000 genomes]
rs12092267	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12097148	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12738355	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13374924	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418442	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986660	0.88[ASN][1000 genomes]
rs2245475	0.81[AMR][1000 genomes]
rs2404718	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2404992	0.88[ASN][1000 genomes]
rs2404993	0.88[ASN][1000 genomes]
rs2746345	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2746348	0.81[AMR][1000 genomes]
rs2746349	0.81[AMR][1000 genomes]
rs2746353	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796517	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796519	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796523	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796527	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4548471	0.88[ASN][1000 genomes]
rs4551620	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4562656	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4584419	0.85[ASN][1000 genomes]
rs59223968	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61772962	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61774287	0.88[ASN][1000 genomes]
rs6588641	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6683935	0.81[AMR][1000 genomes]
rs72666470	0.83[ASN][1000 genomes]
rs7419053	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515414	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519509	0.85[ASN][1000 genomes]
rs7533440	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7545066	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7546264	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547486	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs932447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9887834	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9887940	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv523032	chr1:57116909-57249558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	esv1831276	chr1:57139370-57175158	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	nsv520726	chr1:57143986-57205666	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57122800-57169600	Weak transcription	Ovary	ovary
2	chr1:57125600-57169800	Weak transcription	Aorta	Aorta
3	chr1:57144200-57171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:57144400-57173600	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:57154200-57174800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:57154400-57174600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:57154400-57174800	Weak transcription	Gastric	stomach
8	chr1:57154600-57169800	Weak transcription	Fetal Intestine Large	intestine
9	chr1:57159600-57172800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:57159800-57174800	Weak transcription	Fetal Stomach	stomach
11	chr1:57160000-57174800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:57160200-57174600	Weak transcription	Fetal Brain Male	brain
13	chr1:57160400-57174800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:57162600-57174600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:57162800-57176200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:57166200-57169600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:57166200-57174800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:57166200-57178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:57166400-57169600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:57166400-57171800	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:57166600-57169600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:57166600-57169600	Weak transcription	Fetal Brain Female	brain
23	chr1:57166600-57169600	Weak transcription	Left Ventricle	heart
24	chr1:57166600-57169800	Weak transcription	HepG2	liver
25	chr1:57166600-57171800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:57166600-57175600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:57166600-57175600	Weak transcription	Right Ventricle	heart
28	chr1:57166800-57170000	Weak transcription	Fetal Heart	heart
29	chr1:57167400-57169600	Weak transcription	Pancreas	Pancrea
30	chr1:57169000-57169800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:57169000-57170000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:57169000-57170200	Strong transcription	Hela-S3	cervix
33	chr1:57169000-57174400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:57169200-57170200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:57169200-57170200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
36	chr1:57169200-57170400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:57169200-57170600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr1:57169400-57170000	ZNF genes & repeats	Psoas Muscle	Psoas
39	chr1:57169400-57170000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
40	chr1:57169400-57170000	ZNF genes & repeats	A549	lung
41	chr1:57169400-57170200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:57169400-57170200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:57169400-57170200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr1:57169400-57170200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:57169400-57170200	ZNF genes & repeats	Brain Hippocampus Middle	brain
46	chr1:57169400-57170200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr1:57169400-57170200	ZNF genes & repeats	Fetal Kidney	kidney
48	chr1:57169400-57170200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links