Variant report

Variant	rs6688146
Chromosome Location	chr1:224704397-224704398
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10753474	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916628	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916629	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916630	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916631	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916632	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12093242	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12140117	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12140906	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12141016	0.81[ASN][1000 genomes]
rs12141708	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12142949	0.95[EUR][1000 genomes]
rs12566578	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs1891244	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2648743	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3738367	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4294381	0.89[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs4653589	0.89[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs59319739	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61825792	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6426133	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6665956	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6695773	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6699035	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712065	0.89[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712066	0.94[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7541723	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7541917	0.94[EUR][1000 genomes]
rs7545252	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550648	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs791504	0.90[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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6688146	RAB3GAP2	cis	cerebellum	SCAN
rs6688146	CNIH3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:224696400-224716600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:224699200-224704600	Weak transcription	HSMM	muscle
5	chr1:224701800-224705400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:224701800-224709200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:224701800-224716600	Weak transcription	Ovary	ovary
8	chr1:224702000-224709200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:224702000-224716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:224702200-224716600	Weak transcription	Dnd41	blood
11	chr1:224703200-224707600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:224703400-224711200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:224704000-224705000	Enhancers	K562	blood
14	chr1:224704000-224705200	Enhancers	Fetal Brain Male	brain
15	chr1:224704200-224704800	Enhancers	Fetal Brain Female	brain
16	chr1:224704200-224705000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:224704200-224705800	Enhancers	NH-A	brain
18	chr1:224704200-224706600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links