Variant report

Variant	rs62067558
Chromosome Location	chr17:20025706-20025707
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20024648..20025828-chr17:20223753..20224919,7	MCF-7	breast:
2	chr17:20025221..20027004-chr17:20127712..20130710,2	MCF-7	breast:
3	chr17:20025057..20027504-chr17:20071007..20074000,2	MCF-7	breast:
4	chr17:20025519..20027305-chr17:20058303..20059894,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154898	Chromatin interaction
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1009082	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10438824	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870147	1.00[ASN][1000 genomes]
rs11871827	1.00[ASN][1000 genomes]
rs11871945	1.00[ASN][1000 genomes]
rs12449914	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12451216	0.82[AMR][1000 genomes]
rs12937827	1.00[ASN][1000 genomes]
rs12941200	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943904	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12947950	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948178	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952398	1.00[ASN][1000 genomes]
rs1373147	1.00[ASN][1000 genomes]
rs1544421	1.00[ASN][1000 genomes]
rs1561974	1.00[ASN][1000 genomes]
rs17686622	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686798	0.80[AMR][1000 genomes]
rs17686839	1.00[ASN][1000 genomes]
rs17759609	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17759923	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17759959	0.80[AMR][1000 genomes]
rs1812934	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1985810	1.00[ASN][1000 genomes]
rs1992562	1.00[ASN][1000 genomes]
rs2013441	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2013576	1.00[ASN][1000 genomes]
rs2034109	1.00[ASN][1000 genomes]
rs2080673	1.00[ASN][1000 genomes]
rs2107566	1.00[ASN][1000 genomes]
rs2120282	1.00[ASN][1000 genomes]
rs2158473	1.00[ASN][1000 genomes]
rs2165897	1.00[ASN][1000 genomes]
rs2189710	1.00[ASN][1000 genomes]
rs2243732	1.00[ASN][1000 genomes]
rs2263175	1.00[ASN][1000 genomes]
rs2386429	1.00[ASN][1000 genomes]
rs2386485	1.00[ASN][1000 genomes]
rs2526458	1.00[ASN][1000 genomes]
rs2526460	1.00[ASN][1000 genomes]
rs2526464	1.00[ASN][1000 genomes]
rs2526467	1.00[ASN][1000 genomes]
rs2526468	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526469	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526470	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526471	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526472	1.00[ASN][1000 genomes]
rs2526473	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526474	1.00[ASN][1000 genomes]
rs2526475	1.00[ASN][1000 genomes]
rs2526480	1.00[ASN][1000 genomes]
rs2526483	1.00[ASN][1000 genomes]
rs2526484	1.00[ASN][1000 genomes]
rs2526488	1.00[ASN][1000 genomes]
rs2526490	1.00[ASN][1000 genomes]
rs2526491	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526492	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703772	1.00[ASN][1000 genomes]
rs2703773	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703774	1.00[ASN][1000 genomes]
rs2703778	1.00[ASN][1000 genomes]
rs2703779	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703780	1.00[ASN][1000 genomes]
rs2703782	1.00[ASN][1000 genomes]
rs2703784	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703785	1.00[ASN][1000 genomes]
rs2703787	1.00[ASN][1000 genomes]
rs2703789	1.00[ASN][1000 genomes]
rs2703790	1.00[ASN][1000 genomes]
rs2703791	1.00[ASN][1000 genomes]
rs2703792	1.00[ASN][1000 genomes]
rs2703794	1.00[ASN][1000 genomes]
rs2703797	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703799	1.00[ASN][1000 genomes]
rs2703801	1.00[ASN][1000 genomes]
rs2703802	1.00[ASN][1000 genomes]
rs2703804	1.00[ASN][1000 genomes]
rs2703806	1.00[ASN][1000 genomes]
rs2703808	1.00[ASN][1000 genomes]
rs2703810	1.00[ASN][1000 genomes]
rs2703811	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703813	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703815	1.00[ASN][1000 genomes]
rs2703816	1.00[ASN][1000 genomes]
rs2703817	1.00[ASN][1000 genomes]
rs2703818	1.00[ASN][1000 genomes]
rs2703820	1.00[ASN][1000 genomes]
rs2703821	1.00[ASN][1000 genomes]
rs34089239	1.00[ASN][1000 genomes]
rs34644796	1.00[ASN][1000 genomes]
rs34712254	1.00[ASN][1000 genomes]
rs35103332	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3850783	1.00[ASN][1000 genomes]
rs3850784	1.00[ASN][1000 genomes]
rs3850785	1.00[ASN][1000 genomes]
rs4588033	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4924808	0.80[AMR][1000 genomes]
rs4924809	1.00[ASN][1000 genomes]
rs4924810	1.00[ASN][1000 genomes]
rs4925089	1.00[ASN][1000 genomes]
rs62066869	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587063	0.83[ASN][1000 genomes]
rs6587064	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7207611	1.00[ASN][1000 genomes]
rs7207817	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7223488	0.83[ASN][1000 genomes]
rs8070401	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071665	1.00[ASN][1000 genomes]
rs8074047	1.00[ASN][1000 genomes]
rs8079701	1.00[ASN][1000 genomes]
rs9325894	1.00[ASN][1000 genomes]
rs9892630	1.00[ASN][1000 genomes]
rs9896221	1.00[ASN][1000 genomes]
rs9896709	1.00[ASN][1000 genomes]
rs9897328	1.00[ASN][1000 genomes]
rs9900166	1.00[ASN][1000 genomes]
rs9904928	1.00[ASN][1000 genomes]
rs9905493	1.00[ASN][1000 genomes]
rs9915059	1.00[ASN][1000 genomes]

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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62067558	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:20014600-20028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:20016000-20028800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:20016400-20028600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:20017400-20026200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:20023600-20026000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:20023600-20026600	Enhancers	Fetal Brain Male	brain
9	chr17:20023800-20025800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:20023800-20026000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr17:20024000-20026000	Enhancers	Fetal Muscle Leg	muscle
12	chr17:20024200-20026000	Enhancers	Fetal Brain Female	brain
13	chr17:20024200-20026200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr17:20024400-20025800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr17:20024400-20025800	Enhancers	Fetal Muscle Trunk	muscle
16	chr17:20024400-20025800	Enhancers	Ovary	ovary
17	chr17:20024400-20026200	Enhancers	HSMM	muscle
18	chr17:20024600-20028800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr17:20024800-20025800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:20024800-20025800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:20024800-20026200	Enhancers	Aorta	Aorta
22	chr17:20025000-20026000	Enhancers	Fetal Stomach	stomach
23	chr17:20025000-20026000	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr17:20025000-20026400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr17:20025200-20025800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:20025200-20025800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:20025200-20025800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:20025200-20025800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:20025200-20025800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:20025200-20025800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr17:20025200-20025800	Enhancers	Gastric	stomach
32	chr17:20025200-20025800	Enhancers	Spleen	Spleen
33	chr17:20025200-20025800	Flanking Active TSS	Hela-S3	cervix
34	chr17:20025200-20025800	Enhancers	NHLF	lung
35	chr17:20025200-20026000	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr17:20025200-20026000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr17:20025200-20026000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr17:20025200-20026000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr17:20025200-20026000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr17:20025200-20026000	Flanking Active TSS	Osteobl	bone
41	chr17:20025200-20026200	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr17:20025200-20026200	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr17:20025200-20026200	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr17:20025200-20026800	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr17:20025200-20027000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:20025400-20025800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr17:20025400-20025800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr17:20025400-20026000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr17:20025400-20026200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr17:20025400-20028800	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links