Variant report

Variant	rs12059407
Chromosome Location	chr1:183965737-183965738
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	chr1:183964839..183967146-chr1:183970545..183972322,3	K562	blood:
2	chr1:183961368..183963694-chr1:183965617..183967704,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10752927	0.97[ASN][1000 genomes]
rs10797925	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797926	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797927	0.97[ASN][1000 genomes]
rs10797928	0.97[ASN][1000 genomes]
rs10797929	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797930	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10797932	0.82[ASN][1000 genomes]
rs10911477	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911480	0.97[ASN][1000 genomes]
rs10911481	0.97[ASN][1000 genomes]
rs10911482	0.97[ASN][1000 genomes]
rs10911483	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10911484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911485	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911486	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12021841	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12023778	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12027096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028482	0.97[ASN][1000 genomes]
rs12030903	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12030924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12034897	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12034962	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12042354	0.97[ASN][1000 genomes]
rs12044468	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12060999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064779	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12069197	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12085344	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1475402	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16861859	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1887282	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1887283	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1926866	0.97[ASN][1000 genomes]
rs1926867	0.95[ASN][1000 genomes]
rs1926868	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1998926	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2025807	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2148672	0.97[ASN][1000 genomes]
rs2148678	0.96[ASN][1000 genomes]
rs2182623	0.97[ASN][1000 genomes]
rs2182624	0.97[ASN][1000 genomes]
rs3930248	0.97[ASN][1000 genomes]
rs6662690	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698329	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701930	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7410829	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751410	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv533206	chr1:183861204-184091272	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1006655	chr1:183922288-184186677	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv872583	chr1:183955574-184015663	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:183955000-183971200	Weak transcription	Right Atrium	heart
2	chr1:183958600-183974200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:183958800-183971000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:183961400-183970800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:183963000-183967000	Weak transcription	HMEC	breast
6	chr1:183963000-183969400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:183963800-183966200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:183964000-183966200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:183964000-183966200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:183964000-183966200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:183964000-183966200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:183964000-183966400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:183964200-183966200	Enhancers	Stomach Mucosa	stomach
14	chr1:183964200-183967600	Enhancers	Brain Hippocampus Middle	brain
15	chr1:183964400-183966000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:183964600-183965800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:183964600-183966000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:183964600-183966000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:183964600-183966000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:183964600-183967600	Enhancers	Fetal Heart	heart
21	chr1:183964800-183965800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr1:183965000-183967200	Enhancers	Brain Substantia Nigra	brain
23	chr1:183965200-183965800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:183965200-183965800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:183965200-183965800	Enhancers	Left Ventricle	heart
26	chr1:183965200-183966000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:183965200-183966000	Enhancers	Brain Angular Gyrus	brain
28	chr1:183965200-183966000	Enhancers	Fetal Intestine Large	intestine
29	chr1:183965200-183966000	Enhancers	Fetal Intestine Small	intestine
30	chr1:183965200-183966000	Enhancers	Pancreas	Pancrea
31	chr1:183965200-183966200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr1:183965200-183966200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:183965200-183966200	Enhancers	Brain Cingulate Gyrus	brain
34	chr1:183965200-183966400	Enhancers	Fetal Stomach	stomach
35	chr1:183965200-183967200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:183965200-183967800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:183965400-183965800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:183965400-183966000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:183965400-183966000	Enhancers	Colon Smooth Muscle	Colon
40	chr1:183965400-183966200	Flanking Active TSS	K562	blood
41	chr1:183965600-183966000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:183965600-183967400	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links