Variant report

Variant	rs2050923
Chromosome Location	chr1:179211561-179211562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1078872	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs10913690	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs10913692	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs10913697	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs12130276	0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs12132572	0.82[ASN][1000 genomes]
rs1325195	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1763022	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1807916	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1826183	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1856968	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2066279	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2130576	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2171958	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2171959	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs2306941	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2487563	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493124	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs2636265	0.90[ASN][1000 genomes]
rs2636272	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2636274	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs2636276	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs2636277	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2636278	0.91[GIH][hapmap]
rs2636280	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2636282	0.90[ASN][1000 genomes]
rs2636293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2791940	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2791941	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs2791944	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2791945	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2793790	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2793796	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs2793797	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs2793798	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2793800	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2793801	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2793802	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793803	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2793810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793812	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2793813	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2793816	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs2816166	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2816168	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2816183	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2816184	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2816186	1.00[CHB][hapmap]
rs2816187	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2816190	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs2816191	0.82[EUR][1000 genomes]
rs2816193	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs2816197	0.86[ASN][1000 genomes]
rs2816198	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816199	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816200	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2816201	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2816202	0.86[ASN][1000 genomes]
rs2816203	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2816204	0.86[ASN][1000 genomes]
rs2816207	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2816208	0.90[ASN][1000 genomes]
rs2816211	0.90[ASN][1000 genomes]
rs2816212	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2816213	0.90[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs2816214	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2816218	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3121198	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3122376	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs377785	0.92[ASN][1000 genomes]
rs3813642	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs3813643	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs3829794	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs411266	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs413613	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434283	0.92[ASN][1000 genomes]
rs451088	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs4651013	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs915337	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9425839	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9662858	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9726961	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9728480	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2050923	ASTN1	cis	cerebellum	SCAN
rs2050923	IER5	cis	cerebellum	SCAN
rs2050923	FAM20B	cis	parietal	SCAN
rs2050923	KIAA1614	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179203800-179212400	Weak transcription	HepG2	liver
2	chr1:179210600-179211600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:179211000-179211600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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