Variant report

Variant	rs10789211
Chromosome Location	chr1:67088603-67088604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67088339..67090517-chr1:67091923..67094068,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10493411	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs10889636	0.83[ASW][hapmap];0.84[CHD][hapmap]
rs10889638	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11208908	0.81[ASN][1000 genomes]
rs11208910	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11208916	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11208924	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11208929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11208930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11208937	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs12021913	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12023176	0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs12031054	0.83[ASW][hapmap]
rs12034344	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12039282	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12041930	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046520	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12093843	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12402181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565798	0.87[EUR][1000 genomes]
rs12567556	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1359461	0.93[YRI][hapmap]
rs1373909	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1445578	0.81[TSI][hapmap]
rs1445579	0.81[TSI][hapmap]
rs17129064	0.81[TSI][hapmap]
rs1925342	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs2312153	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3795531	0.91[EUR][1000 genomes]
rs4655498	0.81[ASN][1000 genomes]
rs4655620	0.81[ASN][1000 genomes]
rs6588209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588214	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6680968	0.81[ASN][1000 genomes]
rs6686606	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6687137	0.81[ASN][1000 genomes]
rs6701907	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6701988	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72918447	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512692	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519639	0.89[EUR][1000 genomes]
rs7525509	0.89[JPT][hapmap]
rs7526812	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7535076	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7536188	0.83[ASW][hapmap];0.84[CHD][hapmap]
rs7537440	0.89[JPT][hapmap]
rs7547794	0.89[JPT][hapmap]
rs7547857	0.89[JPT][hapmap]
rs7551301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963140	0.81[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1221	chr1:67047908-67092696	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10789211	SGIP1	cis	cerebellum	SCAN
rs10789211	SGIP1	cis	Whole Blood	GTEx
rs10789211	ITGB3BP	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67058000-67092200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:67066400-67089600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:67071600-67094800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:67082000-67089400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:67084200-67099800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:67084600-67089400	Weak transcription	NHLF	lung
7	chr1:67084800-67089200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:67085000-67088800	Weak transcription	NHDF-Ad	bronchial
9	chr1:67085600-67089400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:67086400-67089600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:67086600-67089400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:67087600-67090400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:67088400-67091000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:67088400-67114200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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