Variant report

Variant	rs9436130
Chromosome Location	chr1:57928401-57928402
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10047071	0.86[JPT][hapmap]
rs10047073	0.86[JPT][hapmap]
rs10493219	0.86[JPT][hapmap]
rs10493225	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10889034	1.00[JPT][hapmap]
rs10889044	0.86[JPT][hapmap]
rs10889047	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207010	1.00[JPT][hapmap]
rs11207011	1.00[JPT][hapmap]
rs11207027	0.82[CHB][hapmap]
rs1155680	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11584169	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585751	0.86[JPT][hapmap]
rs12044871	0.93[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12044874	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12044912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12046102	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12061812	1.00[JPT][hapmap]
rs12087888	1.00[JPT][hapmap]
rs12121490	0.93[ASN][1000 genomes]
rs12128305	1.00[JPT][hapmap]
rs12132685	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136107	0.86[JPT][hapmap]
rs12137169	0.86[JPT][hapmap]
rs12142821	1.00[JPT][hapmap]
rs12240237	0.86[JPT][hapmap]
rs1240442	0.86[JPT][hapmap]
rs12405761	0.86[JPT][hapmap]
rs12407896	0.85[CHB][hapmap]
rs12568449	1.00[JPT][hapmap]
rs12726704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12752978	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1334239	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1334240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357783	0.89[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs1424463	0.84[JPT][hapmap]
rs1424467	0.85[JPT][hapmap]
rs166514	1.00[JPT][hapmap]
rs17115686	0.86[JPT][hapmap]
rs17424216	0.86[JPT][hapmap]
rs17425017	0.86[JPT][hapmap]
rs17425189	1.00[JPT][hapmap]
rs17456661	1.00[JPT][hapmap]
rs17459384	0.86[JPT][hapmap]
rs17459948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2216808	0.86[JPT][hapmap]
rs2405696	0.86[JPT][hapmap]
rs2405994	0.86[JPT][hapmap]
rs267638	1.00[JPT][hapmap]
rs267647	1.00[JPT][hapmap]
rs267650	1.00[JPT][hapmap]
rs2781325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34252256	0.94[ASN][1000 genomes]
rs390203	1.00[JPT][hapmap]
rs3909556	0.86[JPT][hapmap]
rs4279875	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs439378	1.00[JPT][hapmap]
rs4912163	1.00[JPT][hapmap]
rs4912244	0.86[JPT][hapmap]
rs59744820	0.85[ASN][1000 genomes]
rs6669975	1.00[JPT][hapmap]
rs736109	1.00[JPT][hapmap]
rs736110	1.00[JPT][hapmap]
rs746937	1.00[JPT][hapmap]
rs7513076	0.86[JPT][hapmap]
rs7535763	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv870908	chr1:57884310-58037783	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9436130	C8A	cis	cerebellum	SCAN
rs9436130	TMEM59	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57917400-57933800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:57927400-57929400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:57927400-57930200	Weak transcription	NHLF	lung
4	chr1:57927400-57930600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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