Variant report

Variant	rs1727317
Chromosome Location	chr12:123618942-123618943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123617700..123620555-chr12:123634870..123636855,3	MCF-7	breast:
2	chr12:123464971..123468188-chr12:123616401..123619545,3	K562	blood:
3	chr12:123616804..123619547-chr12:123619557..123621511,2	K562	blood:
4	chr12:123616507..123619286-chr12:123631305..123632986,2	K562	blood:
5	chr12:123601284..123602809-chr12:123617657..123619807,2	K562	blood:

Variant related genes	Relation type
ENSG00000150967	Chromatin interaction
ENSG00000182196	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1047158	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051431	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744147	0.94[EUR][1000 genomes]
rs10772993	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772995	0.88[EUR][1000 genomes]
rs10846478	0.88[EUR][1000 genomes]
rs10846486	0.86[EUR][1000 genomes]
rs11057192	0.89[EUR][1000 genomes]
rs1106240	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106241	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1260294	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12817892	0.82[EUR][1000 genomes]
rs12818067	0.82[EUR][1000 genomes]
rs12829456	0.82[EUR][1000 genomes]
rs1402274	0.91[EUR][1000 genomes]
rs1569068	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1615694	0.88[EUR][1000 genomes]
rs1616131	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616181	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617156	0.89[EUR][1000 genomes]
rs1617434	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618679	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621194	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626899	0.87[EUR][1000 genomes]
rs1627724	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630693	0.88[EUR][1000 genomes]
rs1630905	0.89[EUR][1000 genomes]
rs1716156	0.84[EUR][1000 genomes]
rs1716157	0.88[EUR][1000 genomes]
rs1716158	0.82[EUR][1000 genomes]
rs1716159	0.88[EUR][1000 genomes]
rs1716160	0.89[EUR][1000 genomes]
rs1716164	0.86[EUR][1000 genomes]
rs1716165	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716167	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716168	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716170	0.81[EUR][1000 genomes]
rs1716171	0.81[EUR][1000 genomes]
rs1716172	0.83[EUR][1000 genomes]
rs1716173	0.85[EUR][1000 genomes]
rs1716175	0.88[EUR][1000 genomes]
rs1716176	0.91[EUR][1000 genomes]
rs1716177	0.91[EUR][1000 genomes]
rs1716182	0.87[EUR][1000 genomes]
rs1716183	0.93[ASN][1000 genomes]
rs1716185	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727290	0.91[EUR][1000 genomes]
rs1727294	0.97[EUR][1000 genomes]
rs1727296	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1727300	0.86[EUR][1000 genomes]
rs1727302	0.81[EUR][1000 genomes]
rs1727306	0.88[EUR][1000 genomes]
rs1727309	0.90[EUR][1000 genomes]
rs1727310	0.90[EUR][1000 genomes]
rs1727313	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727314	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727315	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727316	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727318	0.90[EUR][1000 genomes]
rs1727320	0.89[EUR][1000 genomes]
rs1727322	0.87[EUR][1000 genomes]
rs1727323	0.89[EUR][1000 genomes]
rs1727324	0.91[EUR][1000 genomes]
rs1727325	0.89[EUR][1000 genomes]
rs1727334	0.81[EUR][1000 genomes]
rs1790086	0.88[EUR][1000 genomes]
rs1790087	0.88[EUR][1000 genomes]
rs1790089	0.91[EUR][1000 genomes]
rs1790090	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790095	0.91[EUR][1000 genomes]
rs1790098	0.91[EUR][1000 genomes]
rs1790100	0.91[EUR][1000 genomes]
rs1790101	0.88[EUR][1000 genomes]
rs1790102	0.88[EUR][1000 genomes]
rs1790108	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790109	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790116	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790119	0.82[EUR][1000 genomes]
rs1790120	0.90[EUR][1000 genomes]
rs1790123	0.90[EUR][1000 genomes]
rs1790124	0.86[EUR][1000 genomes]
rs1790125	0.81[EUR][1000 genomes]
rs1790130	0.87[EUR][1000 genomes]
rs1790131	0.89[EUR][1000 genomes]
rs2049114	0.88[EUR][1000 genomes]
rs2510885	0.94[EUR][1000 genomes]
rs2682425	0.85[EUR][1000 genomes]
rs2682429	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682430	0.87[EUR][1000 genomes]
rs2682431	0.89[EUR][1000 genomes]
rs2682433	0.91[EUR][1000 genomes]
rs2682434	0.89[EUR][1000 genomes]
rs2695476	0.91[EUR][1000 genomes]
rs2695478	0.93[EUR][1000 genomes]
rs2695479	0.91[EUR][1000 genomes]
rs2695480	0.90[EUR][1000 genomes]
rs2695481	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695482	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851435	0.89[EUR][1000 genomes]
rs2851436	0.86[EUR][1000 genomes]
rs2851438	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851441	0.90[EUR][1000 genomes]
rs2851450	0.89[EUR][1000 genomes]
rs2851451	0.89[EUR][1000 genomes]
rs2947099	0.87[EUR][1000 genomes]
rs2950537	0.87[EUR][1000 genomes]
rs3018098	0.91[EUR][1000 genomes]
rs34341465	0.82[EUR][1000 genomes]
rs4372492	0.89[EUR][1000 genomes]
rs58809476	0.82[EUR][1000 genomes]
rs7132277	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs884548	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941305	0.81[EUR][1000 genomes]
rs941306	0.81[EUR][1000 genomes]
rs949142	0.96[EUR][1000 genomes];1.00[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	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1727317	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1727317	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1727317	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs1727317	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1727317	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1727317	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1727317	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:123599200-123624600	Weak transcription	Fetal Brain Female	brain
3	chr12:123605800-123624400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:123607600-123619600	Genic enhancers	Fetal Thymus	thymus
5	chr12:123610000-123620400	Enhancers	Placenta	Placenta
6	chr12:123611400-123624400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:123611800-123624400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:123611800-123624400	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:123611800-123624600	Weak transcription	Aorta	Aorta
10	chr12:123612000-123624000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:123612000-123624600	Weak transcription	NH-A	brain
12	chr12:123613600-123620400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:123614000-123619200	Enhancers	NHEK	skin
14	chr12:123614200-123620400	Enhancers	HMEC	breast
15	chr12:123615400-123620200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:123616400-123624200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:123616600-123619400	Weak transcription	Fetal Lung	lung
18	chr12:123616600-123624200	Weak transcription	Fetal Intestine Large	intestine
19	chr12:123616600-123624400	Weak transcription	Small Intestine	intestine
20	chr12:123616600-123624600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:123616600-123624600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:123616800-123619000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:123616800-123624000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:123616800-123624000	Weak transcription	Osteobl	bone
25	chr12:123616800-123624200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:123616800-123624200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:123616800-123624600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:123617000-123621400	Weak transcription	Hela-S3	cervix
29	chr12:123617000-123621600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:123617000-123621600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:123617000-123621600	Weak transcription	Left Ventricle	heart
32	chr12:123617000-123624000	Weak transcription	Brain Angular Gyrus	brain
33	chr12:123617000-123624000	Weak transcription	Colonic Mucosa	Colon
34	chr12:123617000-123624000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:123617000-123624200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:123617000-123624200	Weak transcription	Brain Anterior Caudate	brain
37	chr12:123617000-123624200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:123617000-123624200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:123617000-123624200	Weak transcription	Right Ventricle	heart
40	chr12:123617000-123624400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:123617000-123624600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:123617000-123624600	Weak transcription	Pancreas	Pancrea
43	chr12:123617200-123619200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:123617200-123619400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:123617200-123621600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:123617200-123621600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:123617200-123624400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:123617400-123619000	Weak transcription	Primary B cells from cord blood	blood
49	chr12:123617400-123619000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:123617400-123620200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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