Variant report

Variant	rs520500
Chromosome Location	chr11:85451938-85451939
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85447296..85450521-chr11:85450822..85453106,4	MCF-7	breast:
2	chr11:85449141..85453316-chr11:85456820..85460896,4	MCF-7	breast:
3	chr11:85449712..85452124-chr11:85536910..85538885,2	MCF-7	breast:
4	chr11:85446570..85449228-chr11:85451047..85454870,3	MCF-7	breast:
5	chr11:85451589..85453294-chr11:85503015..85505521,2	MCF-7	breast:
6	chr11:85449862..85452666-chr3:62852459..62854509,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1445497	0.80[ASN][1000 genomes]
rs475380	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs475491	0.90[ASN][1000 genomes]
rs478089	0.95[ASN][1000 genomes]
rs485485	0.82[AMR][1000 genomes]
rs491867	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493078	0.80[ASN][1000 genomes]
rs496187	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs540063	0.90[ASN][1000 genomes]
rs550404	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs556669	0.88[ASN][1000 genomes]
rs556918	0.82[ASN][1000 genomes]
rs570394	0.87[ASN][1000 genomes]
rs575013	0.87[ASN][1000 genomes]
rs580459	0.88[ASN][1000 genomes]
rs588968	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs589327	0.95[ASN][1000 genomes]
rs594892	0.81[ASN][1000 genomes]
rs596029	0.88[ASN][1000 genomes]
rs597480	0.86[ASN][1000 genomes]
rs630613	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs631410	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs641393	0.86[ASN][1000 genomes]
rs644972	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs647175	0.88[ASN][1000 genomes]
rs647912	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs652615	0.80[ASN][1000 genomes]
rs667275	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs675513	0.88[ASN][1000 genomes]
rs678723	0.95[ASN][1000 genomes]
rs679204	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs680498	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689093	0.92[ASN][1000 genomes]
rs7103790	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7123846	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv898050	chr11:85406915-85499290	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1052123	chr11:85425856-85471132	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv555633	chr11:85426330-85473883	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1036110	chr11:85429074-85471132	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1054027	chr11:85429074-85477283	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv3471508	chr11:85429687-85472395	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3471519	chr11:85429687-85472395	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv555634	chr11:85430397-85464922	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv555635	chr11:85430397-85470893	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv555636	chr11:85431886-85465179	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1042192	chr11:85433687-85464922	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1039118	chr11:85433687-85468605	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1039830	chr11:85433687-85470589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1047001	chr11:85433687-85470941	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv1042942	chr11:85433687-85471132	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv1052732	chr11:85434057-85468605	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv1048844	chr11:85434057-85470941	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv1051644	chr11:85434057-85471132	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv555637	chr11:85435730-85470893	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv555638	chr11:85436303-85458076	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv555639	chr11:85436352-85495269	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv1048750	chr11:85436840-85471132	Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	esv2754674	chr11:85436852-85470852	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	esv2757459	chr11:85436868-85473347	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
30	nsv541112	chr11:85436956-85468985	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
31	nsv541113	chr11:85437155-85468845	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs520500	SYTL2	cis	Nerve Tibial	GTEx
rs520500	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85417600-85453000	Weak transcription	Gastric	stomach
2	chr11:85430400-85459000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:85430400-85480400	Weak transcription	Aorta	Aorta
4	chr11:85430800-85459000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:85431800-85466600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:85432000-85460800	Weak transcription	Fetal Muscle Leg	muscle
7	chr11:85435600-85456400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:85437600-85459800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:85437800-85458000	Weak transcription	HSMM	muscle
10	chr11:85439000-85453400	Weak transcription	Colonic Mucosa	Colon
11	chr11:85441400-85456600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:85441600-85460200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:85442200-85461000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:85444400-85461600	Weak transcription	Lung	lung
15	chr11:85445600-85459800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:85445600-85460200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:85447400-85459200	Weak transcription	NH-A	brain
18	chr11:85447400-85459400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:85447600-85459400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:85448000-85463600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:85448000-85480600	Weak transcription	Fetal Stomach	stomach
22	chr11:85448200-85452400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr11:85448200-85460400	Weak transcription	NHLF	lung
24	chr11:85449000-85453400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:85449200-85452000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr11:85449200-85452800	Weak transcription	Fetal Intestine Large	intestine
27	chr11:85449200-85453000	Weak transcription	Left Ventricle	heart
28	chr11:85449200-85453400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:85449200-85453400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:85449200-85453400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:85449200-85453400	Weak transcription	NHEK	skin
32	chr11:85449200-85454000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:85449200-85454600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:85449200-85455800	Weak transcription	Psoas Muscle	Psoas
35	chr11:85449200-85459800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr11:85449200-85478400	Weak transcription	Right Ventricle	heart
37	chr11:85449400-85453000	Weak transcription	Small Intestine	intestine
38	chr11:85449800-85456000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:85450000-85453200	Weak transcription	Right Atrium	heart
40	chr11:85450200-85452000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr11:85450200-85453400	Weak transcription	Pancreas	Pancrea
42	chr11:85450200-85456400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:85450800-85452200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr11:85450800-85452400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:85450800-85453000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:85450800-85453400	Enhancers	Fetal Thymus	thymus
47	chr11:85450800-85454400	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr11:85451000-85452000	Enhancers	HMEC	breast
49	chr11:85451000-85452400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr11:85451000-85452800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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