Variant report

Variant	rs1777254
Chromosome Location	chr1:210954977-210954978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10863854	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs11119583	0.85[CHB][hapmap]
rs11119588	0.85[ASN][1000 genomes]
rs11119589	0.87[ASN][1000 genomes]
rs1114880	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12022273	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12022312	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12040025	0.85[ASN][1000 genomes]
rs1317255	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1340127	0.85[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1340128	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1343147	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1770212	0.88[ASN][1000 genomes]
rs1770214	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1770215	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1770218	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1770220	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1777244	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1777247	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1777252	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1777255	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1777256	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1777257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1777259	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1777263	0.95[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1890846	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs1891661	0.85[EUR][1000 genomes]
rs1934625	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs1934626	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs1934632	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1934633	0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2798145	0.85[AMR][1000 genomes]
rs2798147	0.85[JPT][hapmap]
rs9429845	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9429848	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873153	chr1:210900481-210994339	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv999018	chr1:210907239-210999306	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv832503	chr1:210948760-211103163	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1777254	KCNH1	cis	cerebellum	SCAN
rs1777254	LOC148696	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210941800-210978000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:210944400-210965800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:210946800-210965800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:210953400-210974400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:210953600-210955000	Weak transcription	Fetal Kidney	kidney
6	chr1:210954400-210955400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:210954600-210955000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:210954600-210955400	Genic enhancers	HSMMtube	muscle
9	chr1:210954800-210955200	Enhancers	Brain Hippocampus Middle	brain
10	chr1:210954800-210955800	Strong transcription	HSMM	muscle

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