Variant report

Variant	rs56294743
Chromosome Location	chr3:112028863-112028864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11923402	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1317295	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1317658	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13316383	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2399419	0.80[EUR][1000 genomes]
rs28615303	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4507229	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682400	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55947719	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56008438	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62264125	0.81[EUR][1000 genomes]
rs62278765	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278768	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278769	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278770	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278771	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278843	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6766013	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6795820	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9810421	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9816969	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9818407	0.80[EUR][1000 genomes]
rs9829698	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837134	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9843666	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9853669	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3336356	chr3:112027218-112031669	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56294743	C6orf106	trans	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112025200-112034600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:112027400-112029800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:112027400-112031400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:112027400-112032800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:112027600-112030800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:112027600-112032800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:112027600-112033000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:112028600-112030000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:112028600-112034000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:112028800-112029000	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links