Variant report

Variant	rs10975898
Chromosome Location	chr9:6919984-6919985
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	chr9:6919963..6921657-chr9:6923857..6925524,2	K562	blood:

Variant related genes	Relation type
ENSG00000107077	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10758810	0.91[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs10815484	0.90[EUR][1000 genomes]
rs10815485	0.90[EUR][1000 genomes]
rs10815486	0.91[CEU][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs10815487	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs10815488	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs10815489	0.89[EUR][1000 genomes]
rs10815493	0.80[EUR][1000 genomes]
rs10975900	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10975912	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10975913	0.88[EUR][1000 genomes]
rs10975917	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10975921	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs10975924	0.80[EUR][1000 genomes]
rs10975937	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12352785	0.91[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1538845	0.86[CEU][hapmap]
rs4740864	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs4742272	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs4742273	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs6477129	0.91[EUR][1000 genomes]
rs6477130	0.91[EUR][1000 genomes]
rs6477132	0.90[EUR][1000 genomes]
rs7022642	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7022938	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7026745	0.90[EUR][1000 genomes]
rs7031585	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7038154	0.93[EUR][1000 genomes]
rs7044390	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7851578	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7852078	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7852362	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7862859	0.90[EUR][1000 genomes]
rs7863791	0.91[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs7868655	0.90[EUR][1000 genomes]
rs7868759	0.90[EUR][1000 genomes]
rs7876040	0.90[EUR][1000 genomes]
rs818902	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
8	nsv1016109	chr9:6712314-6924843	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv831499	chr9:6723287-6930933	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
11	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv892184	chr9:6906384-6985602	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10975898	GLDC	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6889600-6929000	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
3	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:6894000-6921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:6894800-6922000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:6894800-6931600	Weak transcription	Dnd41	blood
7	chr9:6896200-6959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:6897600-6932200	Weak transcription	Small Intestine	intestine
9	chr9:6898200-6921200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:6898200-6928800	Weak transcription	Ovary	ovary
11	chr9:6898200-6930800	Weak transcription	HSMMtube	muscle
12	chr9:6900000-6921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:6900600-6943000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:6901600-6944200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr9:6901800-6922000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:6901800-6931600	Weak transcription	Fetal Intestine Large	intestine
17	chr9:6902000-6923800	Weak transcription	Fetal Intestine Small	intestine
18	chr9:6902800-6931000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:6903000-6921800	Weak transcription	NHEK	skin
20	chr9:6903000-6938600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr9:6903200-6920000	Weak transcription	HSMM	muscle
22	chr9:6906000-6921200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr9:6906400-6933200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:6906600-6938200	Weak transcription	Adipose Nuclei	Adipose
25	chr9:6908800-6942600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:6911400-6920800	Weak transcription	Liver	Liver
27	chr9:6911600-6920000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:6912200-6920000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:6912200-6923800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:6912400-6920000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:6912400-6920000	Weak transcription	Fetal Muscle Leg	muscle
32	chr9:6912400-6920000	Weak transcription	NHDF-Ad	bronchial
33	chr9:6912400-6921000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr9:6912400-6921000	Weak transcription	Fetal Thymus	thymus
35	chr9:6912400-6921200	Weak transcription	Gastric	stomach
36	chr9:6912400-6921200	Weak transcription	Lung	lung
37	chr9:6912400-6921200	Weak transcription	Pancreas	Pancrea
38	chr9:6912400-6922400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:6912400-6923800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:6912400-6923800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:6912400-6927200	Weak transcription	Psoas Muscle	Psoas
42	chr9:6912400-6930800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:6912400-6931000	Weak transcription	Right Ventricle	heart
44	chr9:6912400-6931600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:6912400-6932200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:6912400-6932200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:6912400-6932200	Weak transcription	Spleen	Spleen
48	chr9:6912400-6978400	Weak transcription	Esophagus	oesophagus
49	chr9:6912600-6920400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr9:6912600-6922600	Weak transcription	Brain Hippocampus Middle	brain

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