Variant report

Variant	rs28399511
Chromosome Location	chr10:96580140-96580141
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10509677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509680	0.84[EUR][1000 genomes]
rs1057910	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1057911	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11568732	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1358894	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1409649	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1409650	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1409651	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1409652	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1581735	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17110192	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110194	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110236	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110288	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17110310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110321	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17878382	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17878627	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17878673	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17879263	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17879992	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17884832	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17885052	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17885348	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1853207	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2093433	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28371676	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28371682	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2901822	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3740367	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3758581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814637	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3862008	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3862009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304697	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4638245	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55732648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748010	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55805503	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56083530	0.91[AMR][1000 genomes]
rs57079861	0.95[EUR][1000 genomes]
rs57431619	0.89[ASN][1000 genomes]
rs57584668	0.95[EUR][1000 genomes]
rs57822910	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57957726	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58269717	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58349349	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59826872	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60204155	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60214908	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60378628	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61153799	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61249521	0.93[EUR][1000 genomes]
rs61604699	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7076898	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7077029	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7088784	0.95[EUR][1000 genomes]
rs7094920	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs733115	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74150717	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74150870	0.81[EUR][1000 genomes]
rs74152352	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74152356	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74152357	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74152360	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74152362	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74152364	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74152369	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74154112	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs74154119	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74154124	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7896133	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7901123	0.88[EUR][1000 genomes]
rs7907195	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7910609	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7915727	0.95[EUR][1000 genomes]
rs7917617	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9325473	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332092	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332093	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332098	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332108	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332137	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9332141	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332147	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332157	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332160	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332169	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332175	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332177	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332183	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332187	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332188	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332214	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332217	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332227	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332230	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9332245	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9663112	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9663214	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv1050653	chr10:96407825-96634161	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1037364	chr10:96435433-96634161	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3380017	chr10:96439904-96662339	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1046308	chr10:96441300-96633012	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3344949	chr10:96443874-96666028	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv551955	chr10:96444249-96690371	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv551956	chr10:96446632-96632253	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv534171	chr10:96453830-96612764	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv551957	chr10:96454156-96626682	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1047505	chr10:96468200-96593083	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv540748	chr10:96468200-96593083	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	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
14	nsv895902	chr10:96500106-96619025	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
15	esv3529538	chr10:96522848-96700018	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv3529539	chr10:96522848-96700018	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv3361914	chr10:96522865-96700024	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv523259	chr10:96534584-96693727	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1052578	chr10:96538082-96641949	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
20	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
21	nsv895903	chr10:96548132-96604273	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases
22	nsv895904	chr10:96548132-96609064	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	n/a	n/a	inside rSNPs	diseases
23	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28399511	C10orf129	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96565800-96581600	Weak transcription	Fetal Intestine Large	intestine
2	chr10:96566000-96580200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr10:96566200-96580200	Weak transcription	Liver	Liver
4	chr10:96577000-96580200	Weak transcription	Fetal Intestine Small	intestine

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