Variant report

Variant	rs7761044
Chromosome Location	chr6:70934611-70934612
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1023034	1.00[ASN][1000 genomes]
rs10498872	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10945208	1.00[ASN][1000 genomes]
rs12153933	1.00[ASN][1000 genomes]
rs12190357	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192538	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194091	1.00[ASN][1000 genomes]
rs12194189	1.00[ASN][1000 genomes]
rs12194415	1.00[ASN][1000 genomes]
rs12197487	1.00[ASN][1000 genomes]
rs12197540	1.00[ASN][1000 genomes]
rs12203351	1.00[ASN][1000 genomes]
rs12209467	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212518	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201224	1.00[ASN][1000 genomes]
rs13201233	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201660	1.00[ASN][1000 genomes]
rs13202029	1.00[ASN][1000 genomes]
rs13212724	1.00[ASN][1000 genomes]
rs13216129	1.00[ASN][1000 genomes]
rs13219431	1.00[ASN][1000 genomes]
rs2025995	1.00[ASN][1000 genomes]
rs2025996	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037225	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138659	1.00[ASN][1000 genomes]
rs2182998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35005937	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35796471	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35970582	1.00[ASN][1000 genomes]
rs4342384	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62420318	1.00[ASN][1000 genomes]
rs62421673	1.00[ASN][1000 genomes]
rs642635	0.88[EUR][1000 genomes]
rs6455358	1.00[ASN][1000 genomes]
rs6903986	1.00[ASN][1000 genomes]
rs6935778	1.00[ASN][1000 genomes]
rs7743980	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755873	1.00[ASN][1000 genomes]
rs9446215	1.00[ASN][1000 genomes]
rs9455015	1.00[ASN][1000 genomes]
rs9455017	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026151	chr6:70621616-70946967	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv830683	chr6:70743422-70941190	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7761044	COL9A1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70931400-70934800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:70931400-70961400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:70932400-70938000	Weak transcription	Fetal Brain Female	brain
4	chr6:70932600-70951800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:70933000-70951800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:70933600-70947800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:70934400-70935600	Enhancers	Brain Hippocampus Middle	brain
8	chr6:70934400-70951600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:70934600-70934800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links