Variant report

Variant	rs16929240
Chromosome Location	chr9:9387684-9387685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1007728	0.80[JPT][hapmap]
rs10114748	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.95[ASN][1000 genomes]
rs10114865	0.91[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.95[ASN][1000 genomes]
rs10115635	0.90[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs10116547	0.80[JPT][hapmap]
rs10116551	0.80[JPT][hapmap]
rs10121456	0.80[JPT][hapmap]
rs10124880	0.91[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs10124994	0.95[ASN][1000 genomes]
rs10125719	0.99[ASN][1000 genomes]
rs10125720	0.96[ASN][1000 genomes]
rs10435749	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10435823	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10435824	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs10435825	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10435826	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10435827	0.92[CHB][hapmap]
rs10435828	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10435829	0.91[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs10435830	0.91[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs10511525	0.80[JPT][hapmap]
rs10816103	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10816105	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10816106	0.95[ASN][1000 genomes]
rs10816107	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[ASN][1000 genomes]
rs10816109	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs10816110	0.95[ASN][1000 genomes]
rs10816111	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.95[ASN][1000 genomes]
rs10816113	0.80[JPT][hapmap]
rs10816114	0.80[JPT][hapmap]
rs10816115	0.80[JPT][hapmap]
rs10816116	0.80[JPT][hapmap]
rs10977687	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs10977690	0.82[CEU][hapmap];0.92[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs10977691	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs10977693	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs10977694	0.90[CEU][hapmap];0.89[CHB][hapmap]
rs10977695	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10977696	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10977697	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10977698	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs10977701	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10977703	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10977704	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs10977705	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs10977706	0.94[ASN][1000 genomes]
rs10977707	0.94[ASN][1000 genomes]
rs10977708	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs10977709	0.86[CEU][hapmap];0.92[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.95[ASN][1000 genomes]
rs10977710	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.95[ASN][1000 genomes]
rs10977714	0.80[JPT][hapmap]
rs10977715	0.80[JPT][hapmap]
rs10977718	0.80[JPT][hapmap]
rs10977719	0.80[JPT][hapmap]
rs10977721	0.88[JPT][hapmap]
rs10977724	0.80[JPT][hapmap]
rs10977726	0.80[JPT][hapmap]
rs10977729	0.82[JPT][hapmap]
rs12340793	0.80[JPT][hapmap]
rs13295141	0.80[JPT][hapmap]
rs13300008	0.80[JPT][hapmap]
rs1576970	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs1576971	0.90[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1889099	0.95[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889100	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2382003	0.80[JPT][hapmap]
rs36048836	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3955073	0.91[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap]
rs4008110	0.80[JPT][hapmap]
rs4008112	0.80[JPT][hapmap]
rs4400438	0.86[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];0.95[ASN][1000 genomes]
rs4440683	0.80[JPT][hapmap]
rs4487835	0.80[JPT][hapmap]
rs4584193	0.90[CEU][hapmap]
rs4641122	0.91[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs7469900	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7848652	0.80[JPT][hapmap]
rs7857734	0.82[JPT][hapmap]
rs7858077	0.80[JPT][hapmap]
rs7871026	0.80[JPT][hapmap]
rs7871270	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498066	chr9:8961722-9486652	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv892252	chr9:9164473-9476425	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1025791	chr9:9294304-9626331	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv892258	chr9:9304839-9455711	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018493	chr9:9348853-9395912	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv892260	chr9:9350608-9474970	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1016302	chr9:9355676-9549587	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv539982	chr9:9355676-9549587	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv892261	chr9:9364637-9409606	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
10	nsv892262	chr9:9382331-9445270	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	diseases
11	nsv973833	chr9:9383583-9388587	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
12	nsv1029346	chr9:9385317-9395912	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
13	nsv1015203	chr9:9385317-9435620	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
14	nsv466130	chr9:9385640-9399018	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
15	nsv613307	chr9:9385640-9399018	Flanking Active TSS Active TSS Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
16	nsv1017939	chr9:9386437-9415009	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
17	nsv1033399	chr9:9387684-9417108	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16929240	BCORL2	trans	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9385600-9390800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:9387600-9387800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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