Variant report

Variant	rs1890840
Chromosome Location	chr1:210965121-210965122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1343143	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1770213	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1770216	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1770219	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1770221	0.94[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1770222	0.83[EUR][1000 genomes]
rs1777243	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777245	0.93[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1777246	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1777258	0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777261	0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1777264	0.93[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1890839	0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1934628	0.91[GIH][hapmap];0.88[MEX][hapmap]
rs1934629	0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[EUR][1000 genomes]
rs1934630	0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1934636	0.95[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2798147	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4405188	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4951564	0.82[EUR][1000 genomes]
rs4951615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951640	0.94[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs6658580	0.81[CEU][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6666042	0.94[CEU][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7515909	0.94[CEU][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7546472	0.88[CEU][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9429846	0.85[JPT][hapmap]
rs9429847	0.86[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1890840	IL24	cis	cerebellum	SCAN
rs1890840	CR1L	cis	cerebellum	SCAN
rs1890840	DTL	cis	parietal	SCAN

Chromatin state (count:8 , 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	chr1:210955200-210965400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:210964000-210965400	Weak transcription	HSMMtube	muscle
7	chr1:210964200-210965600	Weak transcription	HSMM	muscle
8	chr1:210965000-210965800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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