Variant report

Variant	rs7339106
Chromosome Location	chr13:95223903-95223904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1112370	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408999	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1572935	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs2275647	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2275648	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298055	0.89[ASW][hapmap]
rs2298058	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs34350725	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405130	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35253817	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35678857	0.99[ASN][1000 genomes]
rs3742107	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3897473	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3897474	0.89[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4473052	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4489873	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs4608209	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773801	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492716	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492717	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492718	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321239	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330873	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7331814	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7981788	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7991607	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997035	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7997333	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998025	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9301979	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301981	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301983	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516434	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9516437	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9516438	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516440	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516441	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516443	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516445	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524545	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524547	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524548	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524549	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524550	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524553	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524554	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524555	1.00[ASW][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524556	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524557	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524559	1.00[ASW][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9556402	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9556403	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9556405	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9561638	1.00[ASN][1000 genomes]
rs9561641	0.84[TSI][hapmap]
rs9561642	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590037	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv562756	chr13:95178317-95238154	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7339106	GPR180	cis	Whole Blood	GTEx
rs7339106	GPR180	cis	Adipose Subcutaneous	GTEx
rs7339106	GPR180	cis	lung	GTEx
rs7339106	GPR180	cis	parietal	SCAN
rs7339106	GPC5	cis	parietal	SCAN
rs7339106	GPR180	cis	Nerve Tibial	GTEx
rs7339106	ZDHHC9	trans	parietal	SCAN
rs7339106	GPR180	cis	cerebellum	SCAN
rs7339106	GPR180	cis	Artery Tibial	GTEx
rs7339106	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs7339106	GPR180	cis	Esophagus Mucosa	GTEx
rs7339106	GPR180	cis	Muscle Skeletal	GTEx
rs7339106	GPR180	cis	Stomach	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95209400-95225000	Weak transcription	HepG2	liver
2	chr13:95210800-95225000	Weak transcription	K562	blood
3	chr13:95211800-95224000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr13:95212800-95225000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr13:95215000-95235400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:95217800-95225400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:95218400-95232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr13:95219200-95238200	Strong transcription	Primary T cells from cord blood	blood
9	chr13:95219600-95237000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:95219600-95245600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr13:95220200-95225600	Strong transcription	Primary B cells from cord blood	blood
12	chr13:95220600-95224200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr13:95220600-95227800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:95220800-95225600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:95220800-95226200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:95220800-95227800	Strong transcription	Thymus	Thymus
17	chr13:95220800-95229200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr13:95220800-95231000	Strong transcription	Liver	Liver
19	chr13:95220800-95237000	Strong transcription	GM12878-XiMat	blood
20	chr13:95220800-95237600	Strong transcription	Fetal Intestine Large	intestine
21	chr13:95221000-95226200	Strong transcription	Fetal Stomach	stomach
22	chr13:95221000-95237000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:95221000-95238000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr13:95221000-95240000	Strong transcription	Fetal Thymus	thymus
25	chr13:95221000-95241000	Strong transcription	Dnd41	blood
26	chr13:95221200-95235600	Strong transcription	Adipose Nuclei	Adipose
27	chr13:95221200-95236600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr13:95221200-95237400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr13:95221200-95238000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr13:95221200-95239200	Weak transcription	Brain Germinal Matrix	brain
31	chr13:95221400-95226200	Strong transcription	Fetal Intestine Small	intestine
32	chr13:95221400-95226200	Strong transcription	Gastric	stomach
33	chr13:95221400-95228000	Strong transcription	Fetal Muscle Leg	muscle
34	chr13:95221400-95235400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:95221400-95237400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:95221400-95242800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr13:95221400-95245800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr13:95221600-95226000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr13:95221600-95226200	Strong transcription	Spleen	Spleen
40	chr13:95221600-95240000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr13:95221800-95224800	Weak transcription	Psoas Muscle	Psoas
42	chr13:95221800-95228600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr13:95221800-95237000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr13:95221800-95239800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr13:95221800-95241200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr13:95222000-95225800	Strong transcription	Esophagus	oesophagus
47	chr13:95222000-95226000	Strong transcription	Pancreas	Pancrea
48	chr13:95222000-95226200	Strong transcription	Lung	lung
49	chr13:95222000-95227200	Strong transcription	Left Ventricle	heart
50	chr13:95222000-95227200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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