Variant report

Variant	rs6799805
Chromosome Location	chr3:160936364-160936365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160929000..160932392-chr3:160935549..160937889,3	K562	blood:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160919833..160921562-chr3:160936344..160938437,2	K562	blood:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12488878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494844	0.80[ASN][1000 genomes]
rs13318781	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1450519	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs4270539	0.80[ASN][1000 genomes]
rs4465984	0.84[JPT][hapmap]
rs4490410	0.82[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs62278055	0.80[ASN][1000 genomes]
rs731363	0.83[CHB][hapmap]
rs73160351	0.87[ASN][1000 genomes]
rs7622060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649959	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290072	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9825118	0.83[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs9831725	0.82[ASN][1000 genomes]
rs9842281	0.80[ASN][1000 genomes]
rs9852919	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9857946	0.87[ASN][1000 genomes]
rs9858399	0.80[ASN][1000 genomes]
rs9878365	0.80[ASN][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6799805	NMD3	cis	parietal	SCAN
rs6799805	PPM1L	cis	cerebellum	SCAN
rs6799805	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160926000-160938400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:160931000-160938600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:160931800-160937200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:160931800-160938400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:160933200-160939000	Weak transcription	Gastric	stomach
6	chr3:160933400-160938600	Weak transcription	Stomach Mucosa	stomach
7	chr3:160933600-160938400	Weak transcription	Fetal Intestine Large	intestine
8	chr3:160935200-160937000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:160935600-160938000	Weak transcription	Hela-S3	cervix
10	chr3:160935600-160938400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:160935800-160938200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:160935800-160938200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:160935800-160938200	Weak transcription	HepG2	liver
14	chr3:160935800-160938200	Weak transcription	NHDF-Ad	bronchial
15	chr3:160935800-160938400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:160935800-160938600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:160936000-160938200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:160936000-160938200	Weak transcription	Osteobl	bone
19	chr3:160936000-160938400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:160936000-160938600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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