Variant report

Variant	rs7549863
Chromosome Location	chr1:76327923-76327924
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	chr1:76327097..76328864-chr1:76332786..76334905,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10732723	1.00[CHB][hapmap]
rs10782558	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10873788	1.00[CHB][hapmap]
rs11161620	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11161626	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11161768	0.80[AFR][1000 genomes]
rs11161792	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11161857	1.00[CHB][hapmap]
rs1144336	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1146646	1.00[CHB][hapmap]
rs1146653	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11588578	1.00[CHB][hapmap]
rs1159214	1.00[CHB][hapmap]
rs12021855	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12090849	1.00[CHB][hapmap]
rs12093623	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12122939	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12127078	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12136360	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12568447	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12723575	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1565717	1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17650138	1.00[CHB][hapmap]
rs1770887	1.00[CHB][hapmap]
rs2029681	1.00[CHB][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2029683	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2172507	1.00[CHB][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2172508	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2347962	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2881786	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4949677	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4949686	1.00[CHB][hapmap]
rs4949885	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5745336	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5745363	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5745381	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5745390	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5745427	1.00[CHB][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745433	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5745442	1.00[CHB][hapmap]
rs5745449	1.00[CHB][hapmap]
rs61770533	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6678348	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6683437	1.00[CHB][hapmap]
rs6699682	1.00[CHB][hapmap]
rs7523573	1.00[CHB][hapmap]
rs7526288	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7538800	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7547056	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs931507	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1795237	chr1:76268573-76383565	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1800125	chr1:76269439-76379497	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1799260	chr1:76269439-76383297	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1847721	chr1:76269439-76383565	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1004669	chr1:76301198-76409451	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv871671	chr1:76304215-76391646	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7549863	MSH4	cis	Esophagus Muscularis	GTEx
rs7549863	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76327400-76328000	Enhancers	H1 Cell Line	embryonic stem cell
2	chr1:76327400-76328000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:76327400-76328000	Strong transcription	Aorta	Aorta
4	chr1:76327600-76328000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:76327800-76328000	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links