Variant report

Variant	rs3824935
Chromosome Location	chr11:101456002-101456003
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	chr11:101453489..101455397-chr11:101455802..101458009,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254506	Chromatin interaction
ENSG00000137672	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10501985	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10895146	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10895147	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11224823	0.92[CEU][hapmap]
rs11224834	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs11224841	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs11224849	0.85[CEU][hapmap]
rs11224851	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs11224857	0.91[CEU][hapmap]
rs11224862	1.00[CEU][hapmap]
rs11224866	0.94[ASN][1000 genomes]
rs11224867	0.91[ASN][1000 genomes]
rs11224868	0.91[ASN][1000 genomes]
rs11224869	0.94[ASN][1000 genomes]
rs11224871	0.94[ASN][1000 genomes]
rs11224872	0.94[ASN][1000 genomes]
rs11224876	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11224879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11224883	0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11224894	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11224898	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11224901	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11224952	0.91[CEU][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11224955	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11224956	0.91[CEU][hapmap];0.85[JPT][hapmap];0.87[MKK][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11224958	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11224961	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11224963	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11224967	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11493972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11512501	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11512686	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11606771	0.94[ASN][1000 genomes]
rs12146595	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12275413	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12361061	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12363566	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12364156	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12366048	0.94[ASN][1000 genomes]
rs12789602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790768	1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792271	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs12796392	0.92[CEU][hapmap]
rs12796523	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12796974	1.00[CEU][hapmap]
rs12797777	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12798819	0.89[CEU][hapmap]
rs12802694	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34013568	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34159741	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34209047	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35456437	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3802829	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3922961	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4378349	0.94[ASN][1000 genomes]
rs4379797	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4394815	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4406798	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4556510	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs66732103	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7103450	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7109847	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120953	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7121108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7126833	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129904	0.94[ASN][1000 genomes]
rs72976306	0.88[AMR][1000 genomes]
rs7479835	0.94[ASN][1000 genomes]
rs7926503	0.84[CEU][hapmap]
rs7938938	0.94[ASN][1000 genomes]
rs7951517	0.94[ASN][1000 genomes]
rs7952280	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556131	chr11:100985777-101480017	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530644	chr11:101010088-101486038	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv898330	chr11:101243644-101722031	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv2754308	chr11:101409790-101502790	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv898331	chr11:101436689-101492630	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1052159	chr11:101439655-101853293	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1051457	chr11:101446705-101837650	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv530645	chr11:101451416-101778666	Bivalent/Poised TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3824935	DYNC2H1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101454600-101458200	Weak transcription	Gastric	stomach
2	chr11:101454800-101462200	Weak transcription	Pancreas	Pancrea
3	chr11:101455800-101457800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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