Variant report

Variant	rs9299415
Chromosome Location	chr9:96931837-96931838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96931258..96933517-chr9:97020161..97023083,3	K562	blood:
2	chr9:96790823..96795467-chr9:96925835..96932235,7	K562	blood:
3	chr9:96573741..96576396-chr9:96929581..96932062,2	K562	blood:
4	chr9:96834076..96836577-chr9:96929876..96932048,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPDC1-7	chr9:96931457-96932304	NONHSAT133286

Variant related genes	Relation type
ENSG00000175787	Chromatin interaction
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10125839	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739972	0.93[AMR][1000 genomes]
rs11792471	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1421134	0.98[ASN][1000 genomes]
rs1833404	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026618	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675279	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2717489	0.85[EUR][1000 genomes]
rs4744322	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7025880	0.98[ASN][1000 genomes]
rs7045890	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7046438	0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7848170	0.81[EUR][1000 genomes]
rs7865735	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3435412	chr9:96924949-96935312	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96927800-96932200	Active TSS	HSMMtube	muscle
2	chr9:96927800-96932600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr9:96927800-96932600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:96927800-96932800	Active TSS	Aorta	Aorta
5	chr9:96927800-96933200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:96928000-96932600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:96928000-96932800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:96928000-96932800	Active TSS	Psoas Muscle	Psoas
9	chr9:96928200-96932800	Active TSS	Right Ventricle	heart
10	chr9:96928200-96932800	Active TSS	HMEC	breast
11	chr9:96929400-96932800	Active TSS	Right Atrium	heart
12	chr9:96929600-96933400	Weak transcription	Spleen	Spleen
13	chr9:96929600-96936400	Weak transcription	Gastric	stomach
14	chr9:96929600-96938800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:96929800-96932400	Transcr. at gene 5' and 3'	A549	lung
16	chr9:96929800-96933400	Weak transcription	Lung	lung
17	chr9:96929800-96933400	Weak transcription	Pancreas	Pancrea
18	chr9:96929800-96936000	Weak transcription	Esophagus	oesophagus
19	chr9:96929800-96944800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:96929800-96948400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:96930000-96932800	Flanking Active TSS	HUVEC	blood vessel
22	chr9:96930000-96933000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:96930000-96933600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:96930000-96936200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:96930200-96932200	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:96930200-96932600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr9:96930200-96933800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr9:96930400-96932400	Enhancers	Brain Germinal Matrix	brain
29	chr9:96930400-96933400	Weak transcription	Small Intestine	intestine
30	chr9:96930400-96935400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr9:96930400-96938200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr9:96930600-96932000	Enhancers	Brain Cingulate Gyrus	brain
33	chr9:96930600-96932400	Enhancers	Fetal Brain Female	brain
34	chr9:96930600-96932600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr9:96930600-96933800	Enhancers	Primary T cells from cord blood	blood
36	chr9:96930600-96934800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:96930600-96935400	Weak transcription	Fetal Thymus	thymus
38	chr9:96930600-96935600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr9:96930600-96935800	Weak transcription	Placenta	Placenta
40	chr9:96930600-96937600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:96930600-96943600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:96930600-96943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr9:96930800-96932200	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr9:96930800-96932200	Enhancers	Fetal Stomach	stomach
45	chr9:96930800-96932400	Genic enhancers	Primary B cells from cord blood	blood
46	chr9:96930800-96932600	Flanking Active TSS	NHEK	skin
47	chr9:96930800-96933400	Weak transcription	Colonic Mucosa	Colon
48	chr9:96930800-96933600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:96931000-96932200	Transcr. at gene 5' and 3'	Hela-S3	cervix
50	chr9:96931000-96932600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--

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