Variant report

Variant	rs12339244
Chromosome Location	chr9:101948052-101948053
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	chr9:101945788..101948395-chr9:101983472..101985266,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALG2-5	chr9:101947868-101948148	NONHSAT133635

Variant related genes	Relation type
ENSG00000106803	Chromatin interaction
ENSG00000119523	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10988742	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10988743	0.89[AFR][1000 genomes]
rs10988745	0.91[AFR][1000 genomes]
rs12336759	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59091994	0.81[AFR][1000 genomes]
rs73653744	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101936600-101949600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:101944600-101949000	Enhancers	GM12878-XiMat	blood
3	chr9:101946200-101949200	Weak transcription	Primary T cells from cord blood	blood
4	chr9:101946400-101951200	Enhancers	Primary B cells from peripheral blood	blood
5	chr9:101947400-101948200	Enhancers	Fetal Muscle Leg	muscle
6	chr9:101947400-101948400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr9:101947400-101948600	Enhancers	Fetal Muscle Trunk	muscle
8	chr9:101947400-101949000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:101947400-101949200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:101947400-101949600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:101947600-101948200	Enhancers	Brain Germinal Matrix	brain
12	chr9:101947600-101948600	Enhancers	Fetal Brain Female	brain
13	chr9:101947600-101948800	Weak transcription	Primary B cells from cord blood	blood
14	chr9:101947600-101950000	Weak transcription	Fetal Brain Male	brain
15	chr9:101947600-101952400	Weak transcription	Lung	lung
16	chr9:101947600-101952400	Weak transcription	Right Atrium	heart
17	chr9:101947600-101952800	Weak transcription	Spleen	Spleen
18	chr9:101947800-101948200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:101947800-101948200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:101947800-101949400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:101947800-101951000	Weak transcription	Fetal Stomach	stomach
22	chr9:101947800-101952000	Weak transcription	HSMMtube	muscle
23	chr9:101948000-101949400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:101948000-101950400	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links