Variant report

Variant	rs3788494
Chromosome Location	chr22:33129932-33129933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11089592	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894453	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1894454	0.98[ASN][1000 genomes]
rs2008206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157135	0.83[JPT][hapmap]
rs2157138	0.99[ASN][1000 genomes]
rs2413145	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2413146	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2413147	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788487	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788488	0.83[JPT][hapmap]
rs3788489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788492	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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];1.00[ASN][1000 genomes]
rs3788495	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3788496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3788497	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3827340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339044	0.83[JPT][hapmap]
rs4821091	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5754240	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs5994613	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998601	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998602	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5998605	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs5998607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606988	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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	nsv1064719	chr22:33028891-33159636	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv588897	chr22:33116314-33139230	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3788494	XBP1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33121800-33141400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:33127800-33133000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:33127800-33133200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr22:33128000-33130400	Weak transcription	Spleen	Spleen
5	chr22:33128400-33132200	Enhancers	Thymus	Thymus
6	chr22:33128400-33135000	Enhancers	Fetal Thymus	thymus
7	chr22:33129200-33130000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:33129400-33130600	Enhancers	Fetal Muscle Trunk	muscle
9	chr22:33129600-33130400	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr22:33129600-33130600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr22:33129600-33130600	Enhancers	Right Atrium	heart
12	chr22:33129600-33130600	Enhancers	HSMMtube	muscle
13	chr22:33129600-33132000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr22:33129600-33132000	Enhancers	Placenta	Placenta
15	chr22:33129800-33130800	Enhancers	Fetal Stomach	stomach

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