Variant report

Variant	rs13092662
Chromosome Location	chr3:67685594-67685595
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67683377..67686449-chr3:67703484..67706242,3	K562	blood:

Variant related genes	Relation type
ENSG00000241316	Chromatin interaction
ENSG00000172340	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11707967	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11712921	0.92[EUR][1000 genomes]
rs11717561	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11719952	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12714500	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13065696	0.96[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13068759	0.90[EUR][1000 genomes]
rs13068996	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13069212	0.91[EUR][1000 genomes]
rs13069251	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13070332	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13076100	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13077262	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13081838	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13083820	0.91[EUR][1000 genomes]
rs13086260	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13090197	0.90[EUR][1000 genomes]
rs13091275	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13091330	0.90[EUR][1000 genomes]
rs13099253	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1376028	0.96[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1376029	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376030	0.96[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1450345	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1814519	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1823476	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2167181	0.91[EUR][1000 genomes]
rs2198015	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2198016	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2218796	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2362453	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2362455	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62256429	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6766403	0.96[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6774971	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6778266	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779395	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6786211	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6787200	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6787642	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6787853	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788874	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6790771	0.96[EUR][1000 genomes]
rs6791337	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6793868	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794625	0.86[EUR][1000 genomes]
rs6797010	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6797460	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6798228	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806285	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806536	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6808106	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71621318	0.91[EUR][1000 genomes]
rs7434004	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610446	0.91[EUR][1000 genomes]
rs7615766	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7639427	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7644842	0.81[EUR][1000 genomes]
rs7647518	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7653350	0.89[EUR][1000 genomes]
rs881948	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs881949	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs935734	0.96[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9811187	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	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	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13092662	SUCLG2	cis	multi-tissue	Pritchard
rs13092662	RP11-81N13.1	cis	Thyroid	GTEx
rs13092662	SUCLG2	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67612400-67697200	Weak transcription	Hela-S3	cervix
2	chr3:67631400-67700200	Weak transcription	K562	blood
3	chr3:67659800-67685600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:67659800-67690600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:67659800-67697400	Weak transcription	Colonic Mucosa	Colon
6	chr3:67660000-67685600	Weak transcription	HSMMtube	muscle
7	chr3:67660000-67686000	Weak transcription	Gastric	stomach
8	chr3:67660000-67697200	Weak transcription	Lung	lung
9	chr3:67660000-67697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:67660600-67691600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:67661200-67685800	Weak transcription	Pancreas	Pancrea
12	chr3:67661200-67704000	Weak transcription	Fetal Kidney	kidney
13	chr3:67661400-67699400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:67661400-67700000	Weak transcription	Ovary	ovary
15	chr3:67661400-67701000	Weak transcription	Fetal Lung	lung
16	chr3:67661400-67704000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:67661600-67703600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:67662600-67693000	Weak transcription	HepG2	liver
19	chr3:67665000-67692800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:67665200-67692000	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:67668200-67687400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:67668400-67699600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:67668600-67696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:67669200-67691800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:67670200-67703400	Weak transcription	Aorta	Aorta
26	chr3:67670400-67687400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:67670400-67694000	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:67670600-67696200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:67670600-67699000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:67670800-67685600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:67670800-67687400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:67670800-67703200	Weak transcription	Adipose Nuclei	Adipose
33	chr3:67671000-67686000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:67671000-67687000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:67671000-67700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:67671400-67692600	Weak transcription	Fetal Intestine Small	intestine
37	chr3:67671800-67697800	Weak transcription	Dnd41	blood
38	chr3:67673800-67696800	Weak transcription	Fetal Intestine Large	intestine
39	chr3:67673800-67703400	Weak transcription	Fetal Thymus	thymus
40	chr3:67674000-67696600	Weak transcription	Fetal Stomach	stomach
41	chr3:67674000-67704000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:67674400-67692000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:67674800-67685600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:67674800-67685600	Weak transcription	Right Ventricle	heart
45	chr3:67675600-67693200	Weak transcription	Brain Substantia Nigra	brain
46	chr3:67675800-67693000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:67676000-67691600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:67678400-67685600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:67680200-67685600	Weak transcription	Psoas Muscle	Psoas
50	chr3:67680400-67688600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links