Variant report

Variant	rs8097125
Chromosome Location	chr18:13005473-13005474
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	chr18:13003454-13005508	K562	blood:	n/a	n/a
2	POLR2A	chr18:13004940-13005754	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12990233..12992753-chr18:13003201..13005792,2	MCF-7	breast:
2	chr18:12946507..12948439-chr18:13003559..13005990,2	K562	blood:

Variant related genes	Relation type
CEP192	TF binding region
ENSG00000101639	Chromatin interaction
ENSG00000266969	Chromatin interaction
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10221326	0.92[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10221384	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs11080620	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11663049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12605638	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12954256	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12955780	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474043	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1786263	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1786270	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1786279	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1787000	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1787003	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1787004	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1787008	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1973779	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28619103	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28641764	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2902856	0.83[CEU][hapmap];0.81[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35790309	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809912	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs472702	0.86[CEU][hapmap]
rs472992	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs473580	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs474337	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475139	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs478006	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs482360	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs482577	0.84[AMR][1000 genomes]
rs490853	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs491349	0.81[AMR][1000 genomes]
rs492723	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs498685	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4995995	0.82[CHB][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs518145	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs527839	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs529620	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs547084	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs554719	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs554854	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs556371	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs556536	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs557846	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs562151	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs565832	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs567031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs569453	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs570505	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs576963	0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs578208	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6505775	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6505776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6505777	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6505780	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs692833	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs692964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71353243	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7226616	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7229870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7233600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7233814	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7234094	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7234960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7236162	0.83[AMR][1000 genomes]
rs7236764	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7237236	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7241536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7243660	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8088313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8089123	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8097038	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9783859	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9783903	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9948139	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9948681	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9949589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9949682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9951698	0.82[AMR][1000 genomes]
rs9952698	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9958369	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9961669	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9964466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9965977	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs8097125	CEP192	cis	Esophagus Muscularis	GTEx
rs8097125	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs8097125	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs8097125	CEP192	cis	Thyroid	GTEx
rs8097125	CEP192	cis	Adipose Subcutaneous	GTEx
rs8097125	CEP192	cis	Esophagus Mucosa	GTEx
rs8097125	CEP192	cis	lung	GTEx
rs8097125	CEP192	cis	Brain Pons	GTEx
rs8097125	CEP192	cis	Artery Tibial	GTEx
rs8097125	CEP192	cis	Whole Blood	GTEx
rs8097125	CEP192	cis	Temporal Cortex	GTEx
rs8097125	CEP192	cis	Stomach	GTEx
rs8097125	CEP192	cis	Artery Aorta	GTEx
rs8097125	CEP192	cis	Nerve Tibial	GTEx
rs8097125	CEP192	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12992600-13031200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:12992800-13008800	Weak transcription	Colonic Mucosa	Colon
3	chr18:12992800-13009200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr18:12992800-13013200	Weak transcription	Fetal Kidney	kidney
5	chr18:12992800-13016000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr18:12993000-13006400	Weak transcription	Fetal Brain Female	brain
7	chr18:12993000-13023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr18:12993200-13006800	Weak transcription	HSMMtube	muscle
9	chr18:12993200-13007000	Weak transcription	Brain Substantia Nigra	brain
10	chr18:12993200-13008400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr18:12993200-13008400	Weak transcription	Osteobl	bone
12	chr18:12993200-13008800	Weak transcription	NHLF	lung
13	chr18:12993400-13006200	Weak transcription	NH-A	brain
14	chr18:12993400-13006600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr18:12993400-13008200	Weak transcription	Brain Angular Gyrus	brain
16	chr18:12993400-13017800	Weak transcription	Stomach Mucosa	stomach
17	chr18:12993600-13011800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr18:12993600-13011800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr18:12993800-13008400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr18:12993800-13008400	Weak transcription	Psoas Muscle	Psoas
21	chr18:12993800-13008400	Weak transcription	HMEC	breast
22	chr18:12993800-13008800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr18:12993800-13009200	Weak transcription	NHDF-Ad	bronchial
24	chr18:12994000-13006000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr18:12995000-13011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr18:12995200-13042000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:12997000-13006600	Weak transcription	Brain Hippocampus Middle	brain
28	chr18:12997000-13008200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr18:12997000-13008600	Weak transcription	Brain Anterior Caudate	brain
30	chr18:12997000-13008800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr18:12997200-13006800	Weak transcription	Right Atrium	heart
32	chr18:12997200-13011200	Weak transcription	Right Ventricle	heart
33	chr18:12997200-13013200	Weak transcription	Small Intestine	intestine
34	chr18:12997400-13008800	Weak transcription	Pancreas	Pancrea
35	chr18:12997400-13015000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr18:12998400-13006800	Weak transcription	Ovary	ovary
37	chr18:12998400-13041600	Strong transcription	Dnd41	blood
38	chr18:12998600-13008600	Weak transcription	Colon Smooth Muscle	Colon
39	chr18:12998800-13006600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr18:12998800-13008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr18:12999000-13007800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr18:12999000-13008800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr18:12999000-13011800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr18:12999200-13039000	Strong transcription	Fetal Thymus	thymus
45	chr18:12999400-13020800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr18:12999400-13021800	Strong transcription	Primary T cells from cord blood	blood
47	chr18:12999600-13005600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr18:12999600-13017200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr18:12999600-13018800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr18:12999800-13006200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links