Variant report

Variant	rs1504029
Chromosome Location	chr11:85265478-85265479
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1072253	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10751126	0.89[ASN][1000 genomes]
rs1118578	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11234359	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1160187	0.82[ASN][1000 genomes]
rs1160188	0.82[ASN][1000 genomes]
rs11603984	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11604028	0.87[ASN][1000 genomes]
rs11605203	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11607685	0.96[ASN][1000 genomes]
rs12420907	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1354397	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1425223	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1504027	0.96[ASN][1000 genomes]
rs158217	0.89[ASN][1000 genomes]
rs166998	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17810659	0.81[ASN][1000 genomes]
rs1806414	0.85[ASN][1000 genomes]
rs184057	0.91[ASN][1000 genomes]
rs1847433	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs185932	0.84[ASN][1000 genomes]
rs1863256	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1954757	0.81[ASN][1000 genomes]
rs207060	0.88[ASN][1000 genomes]
rs2162055	0.82[ASN][1000 genomes]
rs2175189	0.85[ASN][1000 genomes]
rs2512800	0.88[ASN][1000 genomes]
rs2512803	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs286494	0.86[ASN][1000 genomes]
rs286495	0.86[ASN][1000 genomes]
rs286496	0.88[ASN][1000 genomes]
rs286498	0.86[ASN][1000 genomes]
rs286499	0.86[ASN][1000 genomes]
rs286508	0.91[ASN][1000 genomes]
rs286509	0.91[ASN][1000 genomes]
rs286510	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs286512	0.91[ASN][1000 genomes]
rs286521	0.88[ASN][1000 genomes]
rs286522	0.87[ASN][1000 genomes]
rs286523	0.88[ASN][1000 genomes]
rs286524	0.88[ASN][1000 genomes]
rs286525	0.88[ASN][1000 genomes]
rs286526	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs286527	0.85[ASN][1000 genomes]
rs286529	0.84[ASN][1000 genomes]
rs286530	0.86[ASN][1000 genomes]
rs286531	0.89[ASN][1000 genomes]
rs286534	0.88[ASN][1000 genomes]
rs286535	0.85[ASN][1000 genomes]
rs286537	0.89[ASN][1000 genomes]
rs286538	0.91[ASN][1000 genomes]
rs286539	0.91[ASN][1000 genomes]
rs286540	0.91[ASN][1000 genomes]
rs286541	0.91[ASN][1000 genomes]
rs286542	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35097455	0.82[ASN][1000 genomes]
rs4015271	0.80[AFR][1000 genomes]
rs4280023	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4943922	0.97[AFR][1000 genomes]
rs4943923	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944520	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944522	0.84[ASN][1000 genomes]
rs4944523	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4944527	0.81[ASN][1000 genomes]
rs497698	0.82[ASN][1000 genomes]
rs55739259	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55933855	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56073783	0.88[ASN][1000 genomes]
rs56238215	0.87[ASN][1000 genomes]
rs56256400	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56273824	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56321405	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56737296	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57223077	0.88[ASN][1000 genomes]
rs57245119	0.94[AFR][1000 genomes]
rs58757261	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58930391	0.83[ASN][1000 genomes]
rs59082411	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60484561	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60838923	0.83[ASN][1000 genomes]
rs61133973	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61286868	0.87[ASN][1000 genomes]
rs62388	0.89[ASN][1000 genomes]
rs6592252	0.81[ASN][1000 genomes]
rs6592253	0.81[ASN][1000 genomes]
rs7108132	0.81[ASN][1000 genomes]
rs7108137	0.88[ASN][1000 genomes]
rs7115250	0.81[ASN][1000 genomes]
rs7119372	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7122887	0.88[AFR][1000 genomes]
rs73499156	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73499163	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7939217	0.84[ASN][1000 genomes]
rs7948778	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7949567	0.82[AFR][1000 genomes]
rs881121	0.81[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	nsv1044370	chr11:84748993-85293233	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1050363	chr11:85163437-85293233	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541111	chr11:85163437-85293233	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv898046	chr11:85180409-85300458	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv898047	chr11:85180409-85377707	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
10	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv898049	chr11:85231475-85292310	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv518780	chr11:85245772-85266793	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
13	esv3463542	chr11:85262872-85274882	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
14	esv3463553	chr11:85262901-85274878	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
15	esv3463564	chr11:85262929-85274858	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
16	esv3463575	chr11:85263028-85274777	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
17	esv2421768	chr11:85263724-85271345	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
18	esv2829954	chr11:85263724-85271345	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
19	nsv555630	chr11:85263724-85271345	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
20	esv32962	chr11:85264773-85272684	Weak transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1504029	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85248800-85292000	Weak transcription	Aorta	Aorta
2	chr11:85252200-85266400	Weak transcription	Ovary	ovary
3	chr11:85260400-85266400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:85260400-85268600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:85261000-85266200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:85261400-85284000	Weak transcription	Left Ventricle	heart
7	chr11:85263600-85266000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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