Variant report

Variant	rs7875586
Chromosome Location	chr9:95891998-95891999
allele	C/T
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	chr9:95891411-95892042	HL-60	blood:	n/a	n/a
2	POLR2A	chr9:95891355-95892062	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr9:95891621-95892136	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:95891946-95892349	GM12891	blood:	n/a	n/a
5	POLR2A	chr9:95891485-95892838	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:95891614-95892242	GM12892	blood:	n/a	n/a
7	POLR2A	chr9:95891725-95892115	HepG2	liver:	n/a	n/a
8	POLR2A	chr9:95889814-95892543	HepG2	liver:	n/a	n/a
9	NR3C1	chr9:95891790-95892125	A549	lung:	n/a	chr9:95892004-95892018 chr9:95892003-95892018

No.	Distal block	Cell Line	Cell type
1	chr9:95881490..95886849-chr9:95891631..95895235,6	K562	blood:
2	chr9:95857275..95859572-chr9:95888374..95892185,3	MCF-7	breast:
3	chr9:95890205..95893165-chr9:95905253..95907697,2	MCF-7	breast:

Variant related genes	Relation type
NINJ1	TF binding region
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10114849	1.00[AFR][1000 genomes]
rs10992630	0.86[JPT][hapmap]
rs1127851	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11793313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12378451	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs1419232	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs1970623	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2185974	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275848	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3750555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3793662	0.98[ASN][1000 genomes]
rs3829123	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743886	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap]
rs4743895	1.00[ASW][hapmap]
rs4744177	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479454	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs6479455	1.00[AFR][1000 genomes]
rs7847349	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7867718	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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 target site	23 gene(s)	inside rSNPs	diseases
5	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv614879	chr9:95883363-95897564	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7875586	C9orf89	cis	lymphoblastoid	seeQTL
rs7875586	SUSD3	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95870000-95895400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:95871000-95894200	Weak transcription	Dnd41	blood
3	chr9:95883000-95894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:95883000-95895000	Weak transcription	HSMMtube	muscle
5	chr9:95883000-95895000	Weak transcription	K562	blood
6	chr9:95885000-95895400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:95886800-95895400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr9:95887400-95893600	Weak transcription	NHLF	lung
9	chr9:95887600-95894800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr9:95887800-95893400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr9:95887800-95894000	Weak transcription	Brain Germinal Matrix	brain
12	chr9:95888200-95892200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr9:95888200-95893400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:95888200-95893400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr9:95888200-95894600	Weak transcription	Osteobl	bone
16	chr9:95888200-95895000	Enhancers	Esophagus	oesophagus
17	chr9:95888400-95894200	Weak transcription	Hela-S3	cervix
18	chr9:95888400-95894800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr9:95888400-95895000	Enhancers	HUVEC	blood vessel
20	chr9:95888600-95893200	Enhancers	Right Ventricle	heart
21	chr9:95888600-95894200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:95888600-95895000	Enhancers	Brain Cingulate Gyrus	brain
23	chr9:95888600-95895200	Enhancers	Left Ventricle	heart
24	chr9:95888800-95892000	Enhancers	Fetal Muscle Leg	muscle
25	chr9:95888800-95892400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:95888800-95892400	Enhancers	Duodenum Mucosa	Duodenum
27	chr9:95888800-95893800	Enhancers	Primary B cells from cord blood	blood
28	chr9:95888800-95893800	Enhancers	Brain Substantia Nigra	brain
29	chr9:95888800-95895000	Enhancers	Lung	lung
30	chr9:95889000-95893800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:95889200-95893400	Genic enhancers	Gastric	stomach
32	chr9:95889200-95895400	Weak transcription	Thymus	Thymus
33	chr9:95889400-95894400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr9:95889400-95894600	Enhancers	Pancreas	Pancrea
35	chr9:95889400-95894800	Weak transcription	Fetal Brain Male	brain
36	chr9:95889400-95895000	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr9:95889600-95892200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr9:95889600-95893000	Enhancers	Adipose Nuclei	Adipose
39	chr9:95889600-95893400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:95889600-95894800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr9:95889600-95894800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr9:95889600-95895000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:95889600-95895200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:95889800-95893000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:95889800-95893600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:95889800-95893600	Weak transcription	HSMM	muscle
47	chr9:95889800-95894200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:95889800-95894600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:95889800-95895200	Weak transcription	Fetal Kidney	kidney
50	chr9:95890000-95893400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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