Variant report

Variant	rs6798564
Chromosome Location	chr3:180347917-180347918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:180327816..180329534-chr3:180347493..180349979,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16831798	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2338435	0.85[AMR][1000 genomes]
rs34373335	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4854982	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55969409	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58774466	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62292365	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62292366	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62292369	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62292371	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7612917	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][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	nsv1007831	chr3:180162003-180348203	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536818	chr3:180162003-180348203	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers 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	10 gene(s)	inside rSNPs	diseases
3	esv3359190	chr3:180298396-180397223	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6798564	CAMK2N2	cis	parietal	SCAN
rs6798564	EPRS	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180329400-180349400	Weak transcription	Brain Angular Gyrus	brain
2	chr3:180329600-180348600	Weak transcription	Psoas Muscle	Psoas
3	chr3:180331200-180348000	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:180331200-180348000	Weak transcription	NHEK	skin
5	chr3:180331600-180348000	Weak transcription	HUVEC	blood vessel
6	chr3:180331800-180348200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:180331800-180363200	Weak transcription	Brain Anterior Caudate	brain
8	chr3:180332000-180349800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:180332800-180348000	Weak transcription	HMEC	breast
10	chr3:180342600-180348400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:180344600-180348800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:180344600-180348800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:180344600-180349200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:180344600-180349800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:180344800-180351400	Weak transcription	Fetal Brain Female	brain
16	chr3:180344800-180351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:180345000-180352200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:180345000-180361400	Weak transcription	HSMMtube	muscle
19	chr3:180347800-180348800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:180347800-180349200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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