Variant report

Variant	rs12957380
Chromosome Location	chr18:13099249-13099250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:13099197-13099404	K562	blood:	n/a	n/a

Variant related genes	Relation type
CEP192	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10163827	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11080617	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11080618	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11659979	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs11661559	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11661908	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap]
rs11662634	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11662766	0.87[JPT][hapmap]
rs11664213	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11664469	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12327306	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12604538	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12605267	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12607398	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12607919	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12953783	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12960349	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12961596	0.87[ASN][1000 genomes]
rs12963426	0.89[ASN][1000 genomes]
rs12967249	0.82[AMR][1000 genomes]
rs12970503	0.87[ASN][1000 genomes]
rs12970508	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs12971036	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs13381134	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13381779	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1523064	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs17603207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17659689	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17659749	0.89[ASN][1000 genomes]
rs17659896	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1893323	0.81[AMR][1000 genomes]
rs2282540	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282541	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28551661	0.89[ASN][1000 genomes]
rs28654613	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34117444	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34166083	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34302481	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35368962	0.90[ASN][1000 genomes]
rs35563947	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809914	0.82[ASN][1000 genomes]
rs3976787	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs496270	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6505772	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs68004799	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71353241	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7228684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7229869	0.82[EUR][1000 genomes]
rs7230391	0.89[ASN][1000 genomes]
rs7234938	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7236710	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7239486	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8083393	0.87[JPT][hapmap]
rs8083401	0.84[ASN][1000 genomes]
rs8089724	0.91[ASN][1000 genomes]
rs8090667	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs8093236	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs8093576	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8096860	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs8566	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9950241	0.87[ASN][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	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12957380	CEP192	cis	Thyroid	GTEx
rs12957380	CEP192	cis	Esophagus Muscularis	GTEx
rs12957380	CEP192	cis	Artery Tibial	GTEx
rs12957380	CEP192	cis	cerebellum	SCAN
rs12957380	CEP192	cis	lung	GTEx
rs12957380	CEP192	cis	Nerve Tibial	GTEx
rs12957380	CEP192	cis	parietal	SCAN
rs12957380	CEP192	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13018600-13117400	Weak transcription	Stomach Mucosa	stomach
2	chr18:13075400-13105400	Weak transcription	Psoas Muscle	Psoas
3	chr18:13086000-13109400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr18:13086400-13128000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr18:13089400-13122200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr18:13090600-13109200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr18:13091200-13110800	Weak transcription	Right Atrium	heart
8	chr18:13092800-13099400	Strong transcription	Fetal Stomach	stomach
9	chr18:13092800-13106800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr18:13093000-13109400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr18:13093000-13111200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr18:13093400-13111200	Strong transcription	Fetal Muscle Leg	muscle
13	chr18:13094400-13099400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:13094400-13099400	Strong transcription	Lung	lung
15	chr18:13094400-13099400	Strong transcription	Spleen	Spleen
16	chr18:13094600-13100800	Weak transcription	Fetal Heart	heart
17	chr18:13095400-13109600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr18:13096400-13099400	Weak transcription	NH-A	brain
19	chr18:13096800-13105400	Weak transcription	Fetal Brain Male	brain
20	chr18:13097000-13099600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr18:13097000-13101200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:13097000-13101200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr18:13097200-13099400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr18:13097200-13099400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr18:13097200-13099600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr18:13097200-13099600	Weak transcription	HMEC	breast
27	chr18:13097200-13099600	Weak transcription	K562	blood
28	chr18:13097200-13099800	Weak transcription	Fetal Lung	lung
29	chr18:13097200-13100600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:13097200-13100800	Weak transcription	Esophagus	oesophagus
31	chr18:13097200-13100800	Weak transcription	Fetal Intestine Small	intestine
32	chr18:13097200-13100800	Weak transcription	Gastric	stomach
33	chr18:13097200-13101400	Weak transcription	Pancreas	Pancrea
34	chr18:13097200-13103800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr18:13097200-13105000	Weak transcription	NHDF-Ad	bronchial
36	chr18:13097200-13118800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr18:13097400-13099400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr18:13097400-13099400	ZNF genes & repeats	Fetal Intestine Large	intestine
39	chr18:13097400-13099400	Weak transcription	Osteobl	bone
40	chr18:13097400-13099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr18:13097400-13099800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr18:13097400-13099800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr18:13097400-13099800	Weak transcription	HSMM	muscle
44	chr18:13097400-13100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr18:13097400-13100400	Weak transcription	Brain Hippocampus Middle	brain
46	chr18:13097400-13100800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr18:13097400-13101000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr18:13097400-13101000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr18:13097400-13101000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr18:13097400-13101000	Weak transcription	Left Ventricle	heart

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