Variant report

Variant	rs12110683
Chromosome Location	chr6:133854670-133854671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133849510..133851427-chr6:133854380..133855961,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11964505	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11964979	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11968532	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969376	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969485	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969724	0.89[CHB][hapmap]
rs11970169	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17053540	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17053542	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17641157	1.00[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs17643040	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3777867	1.00[CHB][hapmap]
rs3777876	1.00[CHB][hapmap]
rs3777881	0.90[CHB][hapmap]
rs3777886	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822937	0.89[CEU][hapmap]
rs3822938	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4053065	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41286206	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41286212	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865377	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55903152	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59080198	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60337650	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60797218	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67351386	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67720873	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911415	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912858	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6921393	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929938	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6934616	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003668	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7453259	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7743115	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749529	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7767007	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7771096	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7771144	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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	nsv886681	chr6:133833284-133869617	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12110683	RP1-283K11.3	cis	lung	GTEx
rs12110683	SAMD3	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133823200-133869600	Weak transcription	Psoas Muscle	Psoas
2	chr6:133824400-133854800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:133824400-133861600	Weak transcription	Ovary	ovary
4	chr6:133825600-133857200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:133826600-133862400	Weak transcription	Fetal Lung	lung
6	chr6:133837400-133863600	Weak transcription	A549	lung
7	chr6:133845400-133856400	Weak transcription	Fetal Kidney	kidney
8	chr6:133845400-133860400	Weak transcription	HSMMtube	muscle
9	chr6:133847800-133856400	Weak transcription	Hela-S3	cervix
10	chr6:133852400-133854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:133854000-133855000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:133854000-133855200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:133854200-133854800	Strong transcription	Fetal Muscle Leg	muscle
14	chr6:133854600-133856600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:133854600-133857800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links