Variant report

Variant	rs66750836
Chromosome Location	chr9:104212143-104212144
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104160683..104161236-chr9:104211196..104212187,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136870	Chromatin interaction
ENSG00000136897	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2150736	0.89[EUR][1000 genomes]
rs55785343	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55934101	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55956510	0.93[EUR][1000 genomes]
rs57786986	1.00[EUR][1000 genomes]
rs58681636	0.93[EUR][1000 genomes]
rs59291632	0.93[EUR][1000 genomes]
rs59756949	0.93[EUR][1000 genomes]
rs60349154	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66532188	0.93[EUR][1000 genomes]
rs66662619	0.93[EUR][1000 genomes]
rs67190360	0.93[EUR][1000 genomes]
rs67526534	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7035564	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7043814	0.93[EUR][1000 genomes]
rs72743360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743361	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72743362	0.89[EUR][1000 genomes]
rs73501217	0.93[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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv614962	chr9:104204614-104240708	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104211000-104212200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:104211000-104212200	Active TSS	A549	lung
3	chr9:104211200-104212200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr9:104211400-104212200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:104211400-104212200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:104211400-104212200	Active TSS	Colon Smooth Muscle	Colon
7	chr9:104211600-104212200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:104211600-104212200	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr9:104211800-104212200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr9:104211800-104212200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr9:104211800-104212200	Enhancers	Placenta Amnion	Placenta Amnion
12	chr9:104211800-104212200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr9:104212000-104212200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:104212000-104212200	Enhancers	Liver	Liver
15	chr9:104212000-104212200	Enhancers	Brain Hippocampus Middle	brain
16	chr9:104212000-104212200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr9:104212000-104212200	Enhancers	Hela-S3	cervix
18	chr9:104212000-104212800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr9:104212000-104212800	Weak transcription	Fetal Intestine Small	intestine
20	chr9:104212000-104213200	Weak transcription	Right Ventricle	heart
21	chr9:104212000-104213400	Weak transcription	Right Atrium	heart
22	chr9:104212000-104213800	Enhancers	Fetal Intestine Large	intestine
23	chr9:104212000-104216000	Weak transcription	Fetal Heart	heart
24	chr9:104212000-104216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:104212000-104221200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr9:104212000-104241400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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