Variant report

Variant	rs58692133
Chromosome Location	chr1:46067269-46067270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46059543..46063756-chr1:46065868..46068910,6	K562	blood:
2	chr1:45985772..45988873-chr1:46066566..46070131,3	K562	blood:
3	chr1:45810314..45813113-chr1:46064660..46067353,2	K562	blood:
4	chr1:46056677..46058691-chr1:46065641..46067406,2	MCF-7	breast:
5	chr1:46048104..46051380-chr1:46065834..46070517,6	K562	blood:
6	chr1:46064211..46065793-chr1:46066474..46069082,2	K562	blood:
7	chr1:45985746..45988873-chr1:46066734..46072707,7	K562	blood:

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1053941	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579176	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585275	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587918	0.84[EUR][1000 genomes]
rs11587982	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11590549	0.92[EUR][1000 genomes]
rs28412451	0.87[EUR][1000 genomes]
rs28433203	0.87[EUR][1000 genomes]
rs28484896	0.85[EUR][1000 genomes]
rs28584711	0.81[EUR][1000 genomes]
rs3014232	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41310432	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532639	1.00[ASN][1000 genomes]
rs534534	1.00[ASN][1000 genomes]
rs55659201	0.85[EUR][1000 genomes]
rs55951835	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56020747	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067046	1.00[ASN][1000 genomes]
rs56093189	0.82[EUR][1000 genomes]
rs56238114	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56251392	0.81[EUR][1000 genomes]
rs56261438	1.00[ASN][1000 genomes]
rs6429573	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662572	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6662999	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671239	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72688452	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688460	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517111	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541935	0.81[EUR][1000 genomes]
rs7553374	1.00[ASN][1000 genomes]
rs9429173	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
3	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
4	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
5	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
7	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs58692133	CCDC163P	cis	Muscle Skeletal	GTEx
rs58692133	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs58692133	CCDC163P	cis	Esophagus Muscularis	GTEx
rs58692133	CCDC163P	cis	Nerve Tibial	GTEx
rs58692133	CCDC163P	cis	Thyroid	GTEx
rs58692133	CCDC163P	cis	Artery Aorta	GTEx
rs58692133	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs58692133	CCDC163P	cis	Stomach	GTEx
rs58692133	CCDC163P	cis	Esophagus Mucosa	GTEx
rs58692133	CCDC163P	cis	Whole Blood	GTEx
rs58692133	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs58692133	CCDC163P	cis	lung	GTEx
rs58692133	CCDC163P	cis	Heart Left Ventricle	GTEx
rs58692133	CCDC163P	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46051400-46069800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:46052000-46081000	Weak transcription	Small Intestine	intestine
3	chr1:46052200-46084200	Weak transcription	Right Atrium	heart
4	chr1:46052400-46080600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:46052800-46067800	Weak transcription	NHLF	lung
6	chr1:46052800-46078400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:46052800-46081000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:46052800-46086000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:46052800-46089200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:46052800-46099400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:46053600-46086000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:46053800-46071800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:46055000-46085200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:46055200-46090400	Strong transcription	Dnd41	blood
16	chr1:46055800-46071600	Weak transcription	Left Ventricle	heart
17	chr1:46056000-46079000	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:46056200-46071800	Weak transcription	Fetal Brain Male	brain
19	chr1:46056800-46073400	Weak transcription	Right Ventricle	heart
20	chr1:46056800-46074000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:46057000-46072600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:46057400-46073000	Weak transcription	Gastric	stomach
23	chr1:46057400-46081600	Weak transcription	Psoas Muscle	Psoas
24	chr1:46057800-46072200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:46060600-46068600	Weak transcription	Fetal Lung	lung
26	chr1:46060600-46069600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:46060800-46068200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:46060800-46069600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:46060800-46069800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:46060800-46076200	Weak transcription	Esophagus	oesophagus
31	chr1:46061000-46067800	Weak transcription	Fetal Intestine Large	intestine
32	chr1:46061000-46068200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:46061000-46068200	Weak transcription	Thymus	Thymus
34	chr1:46061000-46072600	Weak transcription	Ovary	ovary
35	chr1:46061000-46072800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:46061000-46073000	Weak transcription	Aorta	Aorta
37	chr1:46061000-46073200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:46061000-46073200	Weak transcription	Pancreas	Pancrea
39	chr1:46061000-46073200	Weak transcription	Spleen	Spleen
40	chr1:46061000-46076200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:46061000-46078800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:46061200-46068200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:46061200-46070400	Weak transcription	NHEK	skin
44	chr1:46061200-46070600	Weak transcription	Brain Germinal Matrix	brain
45	chr1:46061400-46067800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:46061400-46068200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:46061400-46068200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:46061400-46068200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:46061400-46068400	Weak transcription	GM12878-XiMat	blood
50	chr1:46061400-46072000	Weak transcription	Stomach Smooth Muscle	stomach

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