Variant report

Variant	rs28371676
Chromosome Location	chr10:96702363-96702364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10509677	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10509678	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10509680	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1057910	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057911	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1581735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110288	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17110310	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17110314	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17110317	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17110321	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17878382	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17878627	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17878673	0.86[EUR][1000 genomes]
rs17879992	0.86[EUR][1000 genomes]
rs17884832	0.86[EUR][1000 genomes]
rs17885052	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17885348	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1853207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2093433	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28371682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28399511	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2901822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3758581	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3862008	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3862009	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4304697	0.86[EUR][1000 genomes]
rs55732648	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55748010	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55805503	0.86[EUR][1000 genomes]
rs57079861	0.82[EUR][1000 genomes]
rs57584668	0.82[EUR][1000 genomes]
rs57822910	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60214908	0.82[EUR][1000 genomes]
rs60378628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61153799	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61249521	0.80[EUR][1000 genomes]
rs61604699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7076898	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7077029	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7088784	0.82[EUR][1000 genomes]
rs733115	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74150717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74152369	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs74154112	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74154119	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74154124	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7901123	0.84[EUR][1000 genomes]
rs7910609	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7915727	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9325473	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332098	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332137	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332141	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332147	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332157	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332160	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332169	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332175	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332177	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332183	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332187	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332188	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332214	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332217	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332227	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332230	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332245	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663112	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9663214	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1035409	chr10:96495177-96832057	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3336672	chr10:96543010-96711519	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1037973	chr10:96563228-96711744	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1047782	chr10:96581094-96718479	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv551962	chr10:96680265-96734339	Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28371676	C10orf129	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96699200-96702800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr10:96700800-96702600	Transcr. at gene 5' and 3'	Liver	Liver
3	chr10:96701200-96702400	ZNF genes & repeats	Fetal Intestine Small	intestine
4	chr10:96702000-96702600	ZNF genes & repeats	Fetal Intestine Large	intestine

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