Variant report

Variant	rs16899467
Chromosome Location	chr8:125259569-125259570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125259085..125259702-chr8:125384481..125385306,2	MCF-7	breast:
2	chr8:125250083..125252599-chr8:125256637..125259576,2	MCF-7	breast:
3	chr8:125258129..125260887-chr8:125283574..125285765,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM65-1	chr8:125259525-125259639	ENSG00000214803

Variant related genes	Relation type
ENSG00000164983	Chromatin interaction
ENSG00000253227	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17360508	0.94[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs55777105	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56306432	0.90[ASN][1000 genomes]
rs72724903	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72724904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv831452	chr8:125099708-125259926	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16899467	ATAD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125250400-125267600	Weak transcription	Fetal Heart	heart
2	chr8:125258000-125259800	Enhancers	Spleen	Spleen
3	chr8:125258400-125282800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:125258800-125260600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr8:125259000-125259600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr8:125259000-125259600	Enhancers	Pancreas	Pancrea
7	chr8:125259000-125259800	Bivalent Enhancer	Adipose Nuclei	Adipose
8	chr8:125259000-125259800	Enhancers	Fetal Muscle Leg	muscle
9	chr8:125259000-125260000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr8:125259000-125260000	Enhancers	NH-A	brain
11	chr8:125259000-125260200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr8:125259000-125260200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr8:125259200-125259600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr8:125259200-125259600	Bivalent Enhancer	Primary B cells from cord blood	blood
15	chr8:125259200-125259600	Enhancers	Stomach Mucosa	stomach
16	chr8:125259200-125259800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr8:125259200-125260000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr8:125259200-125260000	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr8:125259200-125260200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr8:125259200-125260200	Enhancers	A549	lung
21	chr8:125259200-125260400	Enhancers	GM12878-XiMat	blood
22	chr8:125259200-125260800	Enhancers	Primary B cells from peripheral blood	blood
23	chr8:125259400-125259600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr8:125259400-125259600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr8:125259400-125259600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr8:125259400-125259600	Enhancers	Esophagus	oesophagus
27	chr8:125259400-125259600	Enhancers	Left Ventricle	heart
28	chr8:125259400-125259600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr8:125259400-125259600	Enhancers	Rectal Smooth Muscle	rectum
30	chr8:125259400-125259600	Enhancers	Right Ventricle	heart
31	chr8:125259400-125259800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:125259400-125259800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr8:125259400-125259800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr8:125259400-125259800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr8:125259400-125259800	Enhancers	Brain Germinal Matrix	brain
36	chr8:125259400-125259800	Enhancers	Fetal Thymus	thymus
37	chr8:125259400-125259800	Enhancers	Lung	lung
38	chr8:125259400-125259800	Flanking Active TSS	HUVEC	blood vessel
39	chr8:125259400-125259800	Enhancers	K562	blood
40	chr8:125259400-125259800	Flanking Active TSS	Osteobl	bone
41	chr8:125259400-125260000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr8:125259400-125260000	Flanking Active TSS	Hela-S3	cervix
43	chr8:125259400-125260200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr8:125259400-125260200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr8:125259400-125260200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr8:125259400-125260200	Enhancers	Placenta	Placenta
47	chr8:125259400-125260200	Enhancers	HMEC	breast
48	chr8:125259400-125260200	Enhancers	HSMM	muscle
49	chr8:125259400-125260200	Enhancers	NHDF-Ad	bronchial
50	chr8:125259400-125260200	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links