Variant report

Variant	rs478089
Chromosome Location	chr11:85447003-85447004
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85374803..85376402-chr11:85446135..85448325,2	MCF-7	breast:
2	chr11:85435149..85436971-chr11:85444294..85447151,2	MCF-7	breast:
3	chr11:85446235..85448098-chr11:85532932..85535818,2	MCF-7	breast:
4	chr11:85445267..85447565-chr11:85447614..85449688,2	MCF-7	breast:
5	chr11:85446637..85448828-chr11:85475522..85477132,2	MCF-7	breast:
6	chr11:85445028..85447969-chr11:85452486..85454600,2	K562	blood:
7	chr11:85446570..85449228-chr11:85451047..85454870,3	MCF-7	breast:
8	chr11:85445724..85449951-chr11:85518014..85522628,5	MCF-7	breast:
9	chr11:85444504..85447684-chr11:85505412..85508647,3	MCF-7	breast:
10	chr11:85434042..85436173-chr11:85445300..85448317,5	MCF-7	breast:
11	chr11:85445751..85448371-chr11:85941133..85943891,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137504	Chromatin interaction
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10898406	0.82[ASN][1000 genomes]
rs10898415	0.83[ASN][1000 genomes]
rs12362853	0.82[ASN][1000 genomes]
rs1445497	0.84[ASN][1000 genomes]
rs2044391	0.82[ASN][1000 genomes]
rs290173	0.91[EUR][1000 genomes]
rs290174	0.91[EUR][1000 genomes]
rs290190	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs290191	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs290195	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs290202	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs475380	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs475491	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs485485	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs491867	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493078	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs496187	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520500	0.95[ASN][1000 genomes]
rs540063	0.91[ASN][1000 genomes]
rs550404	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs556669	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs556918	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs570394	0.90[ASN][1000 genomes]
rs575013	0.90[ASN][1000 genomes]
rs580459	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs588968	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs589327	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594892	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs596029	0.89[ASN][1000 genomes]
rs597480	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs630613	0.82[ASN][1000 genomes]
rs631410	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs641393	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs644972	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs647175	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs647912	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs652615	0.81[ASN][1000 genomes]
rs667275	0.81[ASN][1000 genomes]
rs675513	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs678723	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679204	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680498	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs683105	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs689093	0.90[ASN][1000 genomes]
rs7123846	0.83[EUR][1000 genomes];0.84[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
rs478089	SYTL2	cis	brain	BrainEAC
rs478089	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85417600-85453000	Weak transcription	Gastric	stomach
2	chr11:85422600-85448600	Weak transcription	Fetal Intestine Large	intestine
3	chr11:85422800-85448200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:85424000-85448600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:85430400-85459000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:85430400-85480400	Weak transcription	Aorta	Aorta
7	chr11:85430800-85447200	Weak transcription	Fetal Stomach	stomach
8	chr11:85430800-85448800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr11:85430800-85459000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:85431400-85451600	Weak transcription	HSMMtube	muscle
11	chr11:85431800-85466600	Weak transcription	Brain Substantia Nigra	brain
12	chr11:85432000-85460800	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:85432200-85448400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:85433800-85448600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:85434800-85448200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr11:85435400-85448600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:85435600-85456400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:85436600-85449200	Weak transcription	Small Intestine	intestine
19	chr11:85436800-85448800	Weak transcription	Left Ventricle	heart
20	chr11:85437000-85447200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:85437600-85451000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:85437600-85451600	Weak transcription	Osteobl	bone
23	chr11:85437600-85459800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:85437800-85458000	Weak transcription	HSMM	muscle
25	chr11:85438000-85448800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:85438400-85448600	Weak transcription	Fetal Kidney	kidney
27	chr11:85438600-85448600	Weak transcription	Stomach Mucosa	stomach
28	chr11:85439000-85453400	Weak transcription	Colonic Mucosa	Colon
29	chr11:85441400-85456600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:85441600-85460200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:85442200-85461000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:85443200-85447400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:85443200-85448600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:85443400-85448800	Weak transcription	Placenta	Placenta
35	chr11:85444000-85448800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr11:85444400-85461600	Weak transcription	Lung	lung
37	chr11:85444600-85448400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr11:85444600-85448600	Weak transcription	Fetal Intestine Small	intestine
39	chr11:85445400-85447600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:85445600-85459800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:85445600-85460200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr11:85445800-85447200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:85445800-85448000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:85445800-85448400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:85446200-85447400	Weak transcription	Primary T cells from cord blood	blood
46	chr11:85446200-85448400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr11:85446200-85448400	Weak transcription	Fetal Heart	heart
48	chr11:85446200-85448800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr11:85446200-85449800	Weak transcription	NHDF-Ad	bronchial
50	chr11:85446400-85448000	Weak transcription	Rectal Mucosa Donor 31	rectum

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