Variant report

Variant	rs12714500
Chromosome Location	chr3:67699941-67699942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67692723..67696784-chr3:67696803..67701487,5	K562	blood:
2	chr3:67696995..67702204-chr3:67702925..67706326,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172340	Chromatin interaction
ENSG00000241316	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11707967	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712921	0.85[EUR][1000 genomes]
rs11717561	0.85[EUR][1000 genomes]
rs11719952	0.87[EUR][1000 genomes]
rs13065696	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13068759	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13068996	0.84[EUR][1000 genomes]
rs13069212	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13069251	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13070332	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076100	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13077262	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13081838	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13083820	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13086260	0.85[EUR][1000 genomes]
rs13090197	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13091275	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13091330	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13092662	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13099253	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1376028	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1376029	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1376030	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1450345	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1473351	0.82[EUR][1000 genomes]
rs1814519	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823476	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167181	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2198015	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2198016	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2218796	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362453	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362454	0.80[AMR][1000 genomes]
rs2362455	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256429	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6766403	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6774971	0.86[EUR][1000 genomes]
rs6778266	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6779395	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786211	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6787200	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6787642	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6787853	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6788874	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790771	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6791337	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6793868	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6797010	0.86[EUR][1000 genomes]
rs6797460	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798228	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806285	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806536	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6808106	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71621318	0.84[EUR][1000 genomes]
rs7434004	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610446	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7615766	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7632886	0.82[EUR][1000 genomes]
rs7639427	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7647518	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653350	0.82[EUR][1000 genomes]
rs881948	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs881949	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs935734	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811187	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv876922	chr3:67635506-67755257	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv428739	chr3:67656829-67730379	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12714500	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL
rs12714500	RP11-81N13.1	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67631400-67700200	Weak transcription	K562	blood
2	chr3:67661200-67704000	Weak transcription	Fetal Kidney	kidney
3	chr3:67661400-67700000	Weak transcription	Ovary	ovary
4	chr3:67661400-67701000	Weak transcription	Fetal Lung	lung
5	chr3:67661400-67704000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:67661600-67703600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:67670200-67703400	Weak transcription	Aorta	Aorta
8	chr3:67670800-67703200	Weak transcription	Adipose Nuclei	Adipose
9	chr3:67671000-67700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:67673800-67703400	Weak transcription	Fetal Thymus	thymus
11	chr3:67674000-67704000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:67681400-67703600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:67681800-67704200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:67686600-67703600	Weak transcription	Fetal Heart	heart
15	chr3:67686600-67704000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:67686800-67703400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:67686800-67703400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:67687800-67703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:67688000-67703400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:67689400-67700600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:67689600-67704000	Weak transcription	Thymus	Thymus
22	chr3:67690800-67700200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:67691800-67700800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:67693400-67700000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:67693400-67703400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:67694200-67700200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:67695800-67703600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:67695800-67704000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:67696600-67701800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:67696800-67702400	Enhancers	Fetal Intestine Large	intestine
31	chr3:67697000-67700000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:67697000-67700800	Enhancers	Osteobl	bone
33	chr3:67697000-67701400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:67697200-67700600	Enhancers	Liver	Liver
35	chr3:67697200-67700800	Enhancers	Psoas Muscle	Psoas
36	chr3:67697200-67701000	Enhancers	Stomach Mucosa	stomach
37	chr3:67697200-67702000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr3:67697200-67703600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:67697400-67700200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:67697400-67704200	Enhancers	Small Intestine	intestine
41	chr3:67697600-67700000	Weak transcription	Colonic Mucosa	Colon
42	chr3:67697600-67700000	Enhancers	HSMM	muscle
43	chr3:67697600-67700400	Enhancers	Placenta Amnion	Placenta Amnion
44	chr3:67697600-67701000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:67697600-67701000	Enhancers	NHDF-Ad	bronchial
46	chr3:67697600-67701600	Weak transcription	Esophagus	oesophagus
47	chr3:67697600-67702000	Enhancers	Right Atrium	heart
48	chr3:67697600-67704200	Weak transcription	Lung	lung
49	chr3:67697800-67700000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:67698000-67700200	Weak transcription	Gastric	stomach

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