Variant report

Variant	rs6479442
Chromosome Location	chr9:95715717-95715718
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95714982..95716673-chr9:95724232..95727468,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127084	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10283409	0.85[EUR][1000 genomes]
rs10992562	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12353227	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4410964	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4424328	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7850247	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6479442	ZNF484	cis	parietal	SCAN
rs6479442	ZNF484	cis	cerebellum	SCAN
rs6479442	SPTLC1	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95710200-95715800	Weak transcription	Spleen	Spleen
2	chr9:95710200-95716400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:95711400-95715800	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr9:95712000-95715800	Weak transcription	Lung	lung
5	chr9:95712000-95717200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:95712200-95715800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr9:95712200-95715800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:95712200-95715800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:95712200-95716000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr9:95712400-95715800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr9:95713200-95715800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr9:95713400-95715800	Weak transcription	Esophagus	oesophagus
13	chr9:95714800-95715800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr9:95714800-95715800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:95714800-95716000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:95714800-95716000	Enhancers	Brain Substantia Nigra	brain
17	chr9:95714800-95716200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:95714800-95716800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr9:95714800-95716800	Enhancers	Fetal Lung	lung
20	chr9:95714800-95716800	Enhancers	Fetal Muscle Leg	muscle
21	chr9:95714800-95717000	Enhancers	Fetal Stomach	stomach
22	chr9:95714800-95717200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr9:95714800-95717400	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr9:95715000-95716000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr9:95715000-95716400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:95715000-95716800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr9:95715000-95716800	Enhancers	Stomach Mucosa	stomach
28	chr9:95715000-95717400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr9:95715200-95715800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:95715200-95716000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:95715200-95716000	Enhancers	Brain Angular Gyrus	brain
32	chr9:95715200-95716000	Bivalent Enhancer	Fetal Heart	heart
33	chr9:95715200-95716200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:95715200-95716200	Enhancers	HMEC	breast
35	chr9:95715200-95716200	Enhancers	NHEK	skin
36	chr9:95715200-95717000	Enhancers	Fetal Muscle Trunk	muscle
37	chr9:95715200-95717000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr9:95715200-95717000	Enhancers	HSMM	muscle
39	chr9:95715200-95717200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr9:95715400-95715800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr9:95715400-95715800	Enhancers	Osteobl	bone
42	chr9:95715400-95716200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:95715400-95716800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:95715400-95717000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:95715400-95717000	Enhancers	Left Ventricle	heart
46	chr9:95715400-95717200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:95715400-95717400	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr9:95715400-95717400	Enhancers	Duodenum Mucosa	Duodenum
49	chr9:95715400-95717800	Weak transcription	Fetal Brain Male	brain
50	chr9:95715400-95732200	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links