Variant report

Variant	rs591579
Chromosome Location	chr9:98640244-98640245
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:98640143-98640299	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98637084..98640693-chr9:98667295..98670393,4	K562	blood:
2	chr9:98638841..98641088-chr9:98696754..98699064,2	K562	blood:

Variant related genes	Relation type
LINC00476	TF binding region
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10121403	1.00[ASN][1000 genomes]
rs10481647	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10739632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10739787	0.86[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10760675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10818017	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10983692	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10983739	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10983773	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10983818	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12004422	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs12375861	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12553442	0.99[ASN][1000 genomes]
rs1410783	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1928253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2117432	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2164156	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2164157	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2770837	0.86[ASN][1000 genomes]
rs583716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs585223	0.94[ASN][1000 genomes]
rs601916	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs615866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs617884	0.92[ASN][1000 genomes]
rs631273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs643815	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6478984	0.84[ASN][1000 genomes]
rs6479036	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs667018	0.86[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs680754	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs683829	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs689749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs689871	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs689979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs690222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs690304	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs690335	0.99[ASN][1000 genomes]
rs690420	0.86[ASN][1000 genomes]
rs690563	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs700963	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7028281	0.88[ASN][1000 genomes]
rs7865593	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7868559	0.93[ASN][1000 genomes]
rs7874897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs816676	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs816681	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9409321	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9409322	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv524894	chr9:98637430-98640244	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs591579	LOC57653	cis	parietal	SCAN
rs591579	C9orf130	cis	cerebellum	SCAN
rs591579	C9orf130	cis	parietal	SCAN
rs591579	CORO2A	cis	cerebellum	SCAN
rs591579	LINC00476	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98637000-98640400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:98637200-98640400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr9:98637200-98640400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:98637200-98640600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr9:98638600-98640400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:98638800-98640400	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr9:98638800-98640600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr9:98638800-98640600	Flanking Active TSS	Dnd41	blood
9	chr9:98638800-98648000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:98638800-98648400	Weak transcription	Lung	lung
11	chr9:98638800-98649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:98638800-98654800	Weak transcription	Esophagus	oesophagus
13	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
14	chr9:98639000-98640400	Enhancers	Small Intestine	intestine
15	chr9:98639000-98640600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr9:98639200-98640400	Flanking Active TSS	GM12878-XiMat	blood
17	chr9:98639200-98644200	Weak transcription	Aorta	Aorta
18	chr9:98639400-98640400	Enhancers	Liver	Liver
19	chr9:98639400-98640400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:98639400-98640400	Enhancers	Fetal Brain Male	brain
21	chr9:98639400-98640400	Enhancers	Fetal Intestine Small	intestine
22	chr9:98639400-98640400	Enhancers	Left Ventricle	heart
23	chr9:98639400-98640600	Enhancers	Brain Angular Gyrus	brain
24	chr9:98639400-98640600	Enhancers	HSMM	muscle
25	chr9:98639400-98641600	Weak transcription	Fetal Kidney	kidney
26	chr9:98639400-98641800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:98639400-98643200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr9:98639400-98643400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:98639400-98644000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:98639400-98647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:98639400-98649000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr9:98639400-98650800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
34	chr9:98639400-98678000	Weak transcription	Ovary	ovary
35	chr9:98639600-98640400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr9:98639600-98640400	Enhancers	Brain Substantia Nigra	brain
37	chr9:98639600-98640400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr9:98639600-98640400	Flanking Active TSS	HepG2	liver
39	chr9:98639600-98640400	Flanking Active TSS	NHLF	lung
40	chr9:98639600-98640600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr9:98639600-98640600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:98639600-98640600	Genic enhancers	Brain Hippocampus Middle	brain
43	chr9:98639600-98640600	Enhancers	Duodenum Mucosa	Duodenum
44	chr9:98639600-98641800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:98639600-98644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr9:98639600-98646200	Weak transcription	HSMMtube	muscle
47	chr9:98639600-98649200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr9:98639800-98640400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:98639800-98640400	Enhancers	Duodenum Smooth Muscle	Duodenum

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