Variant report

Variant	rs11892200
Chromosome Location	chr2:50707858-50707859
allele	C/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:34)

rs_ID	r²[population]
rs10176224	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10180284	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10180935	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10197380	0.81[GIH][hapmap]
rs10205041	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10208370	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865247	0.92[ASN][1000 genomes]
rs13001104	0.87[ASN][1000 genomes]
rs1520455	0.84[CHD][hapmap]
rs1990666	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075233	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075234	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2193062	0.96[ASN][1000 genomes]
rs2193063	0.96[ASN][1000 genomes]
rs2216170	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2216172	0.95[ASN][1000 genomes]
rs34453913	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56796303	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6706713	0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs6707831	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721498	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6724631	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726029	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726267	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726487	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726707	0.92[ASN][1000 genomes]
rs6727327	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7566396	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7578902	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7580777	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs759504	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7598402	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7605064	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7605292	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1010510	chr2:50649641-51011565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv535694	chr2:50649641-51011565	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv532650	chr2:50675808-51136752	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv491644	chr2:50680795-50892906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv498102	chr2:50680795-50937503	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv934040	chr2:50681850-50711452	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv2724	chr2:50688876-50734321	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11892200	MSH6	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50691200-50711600	Weak transcription	Fetal Brain Female	brain
2	chr2:50691200-50716000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:50691600-50718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:50695600-50709400	Weak transcription	Brain Germinal Matrix	brain
5	chr2:50699000-50742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:50704400-50718600	Weak transcription	Fetal Brain Male	brain
7	chr2:50706200-50719000	Weak transcription	Stomach Mucosa	stomach
8	chr2:50706600-50719400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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