Variant report

Variant	rs1543796
Chromosome Location	chr6:28990618-28990619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28988747..28991522-chr6:28994649..28996384,2	K562	blood:

Variant related genes	Relation type
ENSG00000223677	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1005123	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1237485	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1476016	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1794587	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs184093	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2013848	0.88[ASN][1000 genomes]
rs2071785	0.87[ASN][1000 genomes]
rs2071790	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209122	0.82[ASN][1000 genomes]
rs209126	0.82[ASN][1000 genomes]
rs209128	0.82[ASN][1000 genomes]
rs209129	0.82[ASN][1000 genomes]
rs209148	0.80[ASN][1000 genomes]
rs2157312	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2157313	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179648	0.98[ASN][1000 genomes]
rs2187807	0.87[ASN][1000 genomes]
rs2187808	0.87[ASN][1000 genomes]
rs2206040	0.91[AFR][1000 genomes]
rs2206041	0.91[AFR][1000 genomes]
rs2269555	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2394512	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2394548	0.91[AFR][1000 genomes]
rs2765229	0.82[ASN][1000 genomes]
rs3116844	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3116846	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3117332	0.82[AFR][1000 genomes]
rs3117334	0.82[AFR][1000 genomes]
rs3117345	0.91[AFR][1000 genomes]
rs3129097	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3129103	0.82[AFR][1000 genomes]
rs3129145	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3129150	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3129792	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129793	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130717	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3130718	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130810	0.83[AFR][1000 genomes]
rs3130811	0.87[AFR][1000 genomes]
rs3130816	0.91[AFR][1000 genomes]
rs3130841	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130842	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130886	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130889	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130897	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3131070	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3131074	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3131077	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3131102	0.80[EUR][1000 genomes]
rs3135319	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135321	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3135322	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3135323	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135324	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135328	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs381808	0.80[ASN][1000 genomes]
rs4427026	0.88[ASN][1000 genomes]
rs4713186	0.84[ASN][1000 genomes]
rs4713187	0.84[ASN][1000 genomes]
rs4713188	0.86[ASN][1000 genomes]
rs4713190	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4713192	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4947339	0.88[ASN][1000 genomes]
rs6456876	0.87[ASN][1000 genomes]
rs6456880	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6456883	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6456891	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6900967	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6901599	0.87[ASN][1000 genomes]
rs6904975	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6906909	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6914955	0.87[ASN][1000 genomes]
rs6916161	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6920392	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6931823	0.88[ASN][1000 genomes]
rs719746	0.91[AFR][1000 genomes]
rs763009	0.87[ASN][1000 genomes]
rs7743189	0.87[ASN][1000 genomes]
rs7761547	0.88[ASN][1000 genomes]
rs7768299	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9257401	0.88[ASN][1000 genomes]
rs9257404	0.87[ASN][1000 genomes]
rs9257405	0.86[ASN][1000 genomes]
rs9257421	0.86[ASN][1000 genomes]
rs9257447	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9257449	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9257455	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9257461	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9257464	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9348816	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9348817	0.86[AMR][1000 genomes]
rs9380109	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9393939	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9393942	0.82[ASN][1000 genomes]
rs9468467	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9468472	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9468480	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv1023028	chr6:28956136-29343575	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv538170	chr6:28956136-29343575	ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
15	nsv1018937	chr6:28956136-29366175	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv1032468	chr6:28968930-29155749	Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv1026403	chr6:28981639-29343575	Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
18	nsv538171	chr6:28981639-29343575	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
19	nsv601216	chr6:28984512-29192146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	nsv830623	chr6:28989707-29171385	Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1543796	NKAPL	cis	parietal	SCAN
rs1543796	ZSCAN23	cis	parietal	SCAN
rs1543796	ZSCAN16	cis	parietal	SCAN
rs1543796	ZNF323	cis	parietal	SCAN
rs1543796	ZKSCAN3	cis	cerebellum	SCAN
rs1543796	ZNF323	cis	cerebellum	SCAN
rs1543796	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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