Variant report

Variant	rs7547056
Chromosome Location	chr1:76279267-76279268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76277185..76279387-chr1:76282606..76285233,2	K562	blood:
2	chr1:76259303..76263920-chr1:76276444..76279468,6	K562	blood:
3	chr1:76277873..76279387-chr1:76283733..76285650,2	K562	blood:
4	chr1:76252079..76256078-chr1:76276265..76280067,4	K562	blood:

Variant related genes	Relation type
ENSG00000206620	Chromatin interaction
ENSG00000207241	Chromatin interaction
ENSG00000057468	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000201487	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10732723	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10782558	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs11161510	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs11161511	0.82[TSI][hapmap]
rs11161521	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs11161620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161626	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161792	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11161836	0.83[CEU][hapmap]
rs11161857	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap]
rs1144336	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146579	0.82[TSI][hapmap]
rs1146581	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs1146646	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146653	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588578	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs1159214	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs12021855	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12090849	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.82[MKK][hapmap]
rs12093623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094842	0.83[EUR][1000 genomes]
rs12122939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123977	0.82[TSI][hapmap]
rs12127078	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134854	0.81[TSI][hapmap]
rs12136360	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568447	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12723575	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1565717	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650138	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap]
rs1770885	0.85[CEU][hapmap]
rs1770887	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs1858536	0.81[TSI][hapmap]
rs2029681	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2029683	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2172507	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2172508	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.84[EUR][1000 genomes]
rs2275378	0.82[TSI][hapmap]
rs2347962	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28602663	0.80[AMR][1000 genomes]
rs2881786	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3818855	0.82[TSI][hapmap]
rs4646961	0.82[TSI][hapmap]
rs4949677	0.91[CEU][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949686	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs4949874	0.81[TSI][hapmap]
rs4949879	0.80[AMR][1000 genomes]
rs4949885	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267813	0.81[EUR][1000 genomes]
rs5745336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745363	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745381	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5745390	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5745427	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5745433	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5745442	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs5745449	1.00[CHB][hapmap]
rs61770533	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799990	0.84[EUR][1000 genomes]
rs6678348	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6683437	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs6699682	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap]
rs7518038	0.81[TSI][hapmap]
rs7523573	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs7534754	0.84[TSI][hapmap]
rs7538800	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7549863	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs931507	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs9662166	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7547056	MSH4	cis	Artery Tibial	GTEx
rs7547056	MSH4	cis	Esophagus Muscularis	GTEx
rs7547056	SNORD45B	cis	parietal	SCAN
rs7547056	MSH4	cis	parietal	SCAN
rs7547056	ACADM	cis	cerebellum	SCAN
rs7547056	ACADM	cis	Whole Blood	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76262400-76282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:76262600-76288800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:76262600-76294600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:76263000-76287400	Weak transcription	Aorta	Aorta
5	chr1:76263000-76289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:76263000-76296200	Weak transcription	Ovary	ovary
7	chr1:76263400-76289000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:76263600-76284000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:76264200-76279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:76264200-76291400	Weak transcription	Psoas Muscle	Psoas
11	chr1:76264600-76288600	Weak transcription	Left Ventricle	heart
12	chr1:76264800-76288600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:76264800-76288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:76278800-76279600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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