Variant report

Variant	rs653565
Chromosome Location	chr11:64212843-64212844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10897503	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs12362958	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28680814	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930353	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs548333	0.82[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs562560	0.84[EUR][1000 genomes]
rs61884054	0.81[EUR][1000 genomes]
rs653578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7119252	0.98[ASN][1000 genomes]
rs72929971	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[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	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv555194	chr11:64189110-64238023	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs653565	TMEM179B	cis	parietal	SCAN
rs653565	SLC3A2	cis	cerebellum	SCAN
rs653565	ESRRA	cis	cerebellum	SCAN
rs653565	RBM14	cis	parietal	SCAN
rs653565	DRAP1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64208400-64215800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:64209800-64215400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:64209800-64215800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:64210000-64213000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr11:64210200-64215000	Weak transcription	Primary B cells from cord blood	blood
6	chr11:64210600-64216200	Weak transcription	Right Atrium	heart
7	chr11:64210800-64215200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr11:64211400-64215000	Weak transcription	Fetal Brain Female	brain
9	chr11:64211600-64215200	Weak transcription	Fetal Brain Male	brain
10	chr11:64211800-64215200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr11:64212000-64213000	Enhancers	Brain Hippocampus Middle	brain
12	chr11:64212400-64213200	Enhancers	GM12878-XiMat	blood
13	chr11:64212400-64213400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:64212600-64213000	Enhancers	Brain Substantia Nigra	brain
15	chr11:64212600-64213200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:64212600-64214400	Weak transcription	Fetal Muscle Leg	muscle
17	chr11:64212600-64215200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:64212800-64215200	Weak transcription	Placenta	Placenta
19	chr11:64212800-64216000	Weak transcription	Spleen	Spleen

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links