Variant report

Variant	rs73396489
Chromosome Location	chr6:24827368-24827369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs16889632	0.89[EUR][1000 genomes]
rs34016544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34298086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45619241	0.90[EUR][1000 genomes]
rs58233236	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61733143	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6899341	0.89[EUR][1000 genomes]
rs6917709	0.82[EUR][1000 genomes]
rs6940247	0.89[EUR][1000 genomes]
rs73396497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73398404	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73398412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7751675	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9467275	0.89[EUR][1000 genomes]
rs9467329	0.82[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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv508396	chr6:24779648-24846309	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24777000-24847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
3	chr6:24788000-24832000	Weak transcription	Brain Substantia Nigra	brain
4	chr6:24788800-24848200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:24789200-24842600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:24798200-24827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:24798200-24841200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:24800000-24843200	Weak transcription	Liver	Liver
9	chr6:24802600-24834200	Weak transcription	HSMM	muscle
10	chr6:24802800-24827400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:24803400-24827400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:24804800-24858200	Weak transcription	Gastric	stomach
13	chr6:24806200-24842400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:24808800-24845600	Weak transcription	Fetal Stomach	stomach
15	chr6:24809800-24827400	Weak transcription	GM12878-XiMat	blood
16	chr6:24809800-24839200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:24810000-24827400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:24810000-24831600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:24810000-24832600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:24810200-24827400	Weak transcription	Brain Germinal Matrix	brain
21	chr6:24810600-24827400	Weak transcription	Left Ventricle	heart
22	chr6:24810600-24827400	Weak transcription	Lung	lung
23	chr6:24817800-24827600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr6:24817800-24829600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:24817800-24836000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:24817800-24839600	Strong transcription	Primary T cells from cord blood	blood
27	chr6:24817800-24840800	Strong transcription	Primary B cells from peripheral blood	blood
28	chr6:24817800-24854400	Strong transcription	Primary B cells from cord blood	blood
29	chr6:24817800-24855800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:24818000-24827800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:24818000-24836200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:24818000-24840000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:24818000-24840600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:24818000-24840600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:24818600-24855800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:24818800-24856000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr6:24818800-24856400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr6:24821400-24834400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:24821400-24836000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr6:24821600-24828200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:24821800-24827800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:24821800-24828400	Strong transcription	Fetal Thymus	thymus
43	chr6:24822200-24827400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:24822400-24827400	Weak transcription	Pancreas	Pancrea
45	chr6:24822400-24840200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:24822600-24844000	Weak transcription	Fetal Heart	heart
47	chr6:24823000-24833400	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:24823000-24835200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:24823400-24828800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:24823800-24827600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links