Variant report

Variant	rs7992691
Chromosome Location	chr13:50189313-50189314
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1198421	0.88[ASN][1000 genomes]
rs1198422	0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs1359542	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1536192	0.86[ASW][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1536195	0.82[EUR][1000 genomes]
rs1570883	0.81[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1886793	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1998780	0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1998781	0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2104183	0.85[CEU][hapmap];0.83[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146145	0.85[CEU][hapmap];0.83[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2209506	0.86[EUR][1000 genomes]
rs2274278	0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2274284	0.86[ASW][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2407697	0.82[MEX][hapmap];0.93[TSI][hapmap]
rs3794376	0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4572288	0.86[ASN][1000 genomes]
rs4941648	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941650	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5007254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561540	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6561542	0.82[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs7139724	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7324024	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7986405	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7986690	0.83[JPT][hapmap]
rs7989286	0.82[EUR][1000 genomes]
rs7994516	0.85[EUR][1000 genomes]
rs7996012	0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8000962	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526577	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535262	0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535269	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9596161	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7992691	RCBTB1	cis	cerebellum	SCAN
rs7992691	RCBTB1	cis	parietal	SCAN
rs7992691	CAB39L	cis	cerebellum	SCAN
rs7992691	CYSLTR2	cis	cerebellum	SCAN
rs7992691	ARL11	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50181200-50192000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr13:50181400-50194400	Weak transcription	Right Ventricle	heart
3	chr13:50183800-50190200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr13:50184600-50193000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:50189200-50192800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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