Variant report

Variant	rs7330899
Chromosome Location	chr13:95223400-95223401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16949940	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs17196177	1.00[CHD][hapmap]
rs2226078	1.00[CHD][hapmap]
rs55960139	0.85[AMR][1000 genomes]
rs61965607	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6492722	1.00[CHD][hapmap]
rs7322453	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs7331837	1.00[CHD][hapmap]
rs7336371	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7984105	1.00[CHD][hapmap]
rs7997429	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8001569	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9301978	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9516436	0.85[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[EUR][1000 genomes]
rs9524538	0.84[EUR][1000 genomes]
rs9524552	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9524570	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9590036	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9590039	0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.87[EUR][1000 genomes]
rs9590043	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7330899	GPR180	cis	parietal	SCAN
rs7330899	GPR180	cis	cerebellum	SCAN
rs7330899	DCT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95202800-95223600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:95209400-95225000	Weak transcription	HepG2	liver
3	chr13:95210800-95225000	Weak transcription	K562	blood
4	chr13:95211800-95224000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr13:95212200-95223600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:95212400-95223400	Weak transcription	HSMM	muscle
7	chr13:95212600-95223600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr13:95212800-95225000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr13:95215000-95235400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:95217800-95225400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr13:95218400-95232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr13:95219200-95238200	Strong transcription	Primary T cells from cord blood	blood
13	chr13:95219600-95237000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:95219600-95245600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:95220200-95225600	Strong transcription	Primary B cells from cord blood	blood
16	chr13:95220600-95224200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr13:95220600-95227800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr13:95220800-95223400	Weak transcription	Brain Angular Gyrus	brain
19	chr13:95220800-95225600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:95220800-95226200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:95220800-95227800	Strong transcription	Thymus	Thymus
22	chr13:95220800-95229200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:95220800-95231000	Strong transcription	Liver	Liver
24	chr13:95220800-95237000	Strong transcription	GM12878-XiMat	blood
25	chr13:95220800-95237600	Strong transcription	Fetal Intestine Large	intestine
26	chr13:95221000-95223600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:95221000-95223600	Weak transcription	Stomach Mucosa	stomach
28	chr13:95221000-95226200	Strong transcription	Fetal Stomach	stomach
29	chr13:95221000-95237000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr13:95221000-95238000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr13:95221000-95240000	Strong transcription	Fetal Thymus	thymus
32	chr13:95221000-95241000	Strong transcription	Dnd41	blood
33	chr13:95221200-95235600	Strong transcription	Adipose Nuclei	Adipose
34	chr13:95221200-95236600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr13:95221200-95237400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr13:95221200-95238000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:95221200-95239200	Weak transcription	Brain Germinal Matrix	brain
38	chr13:95221400-95223600	Weak transcription	HSMMtube	muscle
39	chr13:95221400-95223600	Weak transcription	NHDF-Ad	bronchial
40	chr13:95221400-95226200	Strong transcription	Fetal Intestine Small	intestine
41	chr13:95221400-95226200	Strong transcription	Gastric	stomach
42	chr13:95221400-95228000	Strong transcription	Fetal Muscle Leg	muscle
43	chr13:95221400-95235400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr13:95221400-95237400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr13:95221400-95242800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr13:95221400-95245800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr13:95221600-95223400	Weak transcription	Brain Anterior Caudate	brain
48	chr13:95221600-95226000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr13:95221600-95226200	Strong transcription	Spleen	Spleen
50	chr13:95221600-95240000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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