Variant report

Variant	rs11682957
Chromosome Location	chr2:171727200-171727201
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11694200	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904750	0.81[JPT][hapmap]
rs12467411	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12999141	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17505447	0.82[JPT][hapmap]
rs17752922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081767	0.81[JPT][hapmap]
rs2356422	0.82[JPT][hapmap]
rs3731993	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3770436	0.81[JPT][hapmap]
rs7561915	0.92[EUR][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	nsv508179	chr2:171708404-171736003	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11682957	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171699000-171730000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:171717000-171729400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:171718200-171729400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:171718400-171729200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:171718600-171729400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:171718600-171729600	Weak transcription	Right Atrium	heart
7	chr2:171725800-171729600	Weak transcription	HMEC	breast
8	chr2:171726000-171729600	Weak transcription	NHEK	skin
9	chr2:171726200-171729400	Weak transcription	Primary T cells from cord blood	blood
10	chr2:171726200-171729600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:171726400-171729600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:171727200-171727400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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