Variant report

Variant	rs556918
Chromosome Location	chr11:85486866-85486867
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85471983..85474269-chr11:85484169..85487158,2	MCF-7	breast:
2	chr11:85484461..85487220-chr11:85491729..85494428,2	MCF-7	breast:
3	chr11:85473245..85476644-chr11:85486524..85489414,3	MCF-7	breast:
4	chr11:85484288..85486316-chr11:85486416..85488624,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10898406	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898410	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898413	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898414	0.87[ASN][1000 genomes]
rs10898415	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11606656	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs12362853	0.97[ASN][1000 genomes]
rs1445497	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1481700	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs188311	0.87[CEU][hapmap]
rs1893163	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2008890	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2044391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2044392	0.90[ASN][1000 genomes]
rs2374683	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290173	0.84[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs290174	0.83[EUR][1000 genomes]
rs290175	0.88[CEU][hapmap]
rs290190	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs290191	0.84[EUR][1000 genomes]
rs290194	0.84[CEU][hapmap]
rs290195	0.92[CEU][hapmap];0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs290196	0.88[CEU][hapmap]
rs290199	0.92[CEU][hapmap]
rs290200	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap]
rs290202	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs370385	0.81[JPT][hapmap]
rs475380	0.83[ASN][1000 genomes]
rs475491	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs478089	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs485485	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491867	0.87[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap]
rs493078	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944538	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs496187	0.87[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs510948	0.87[CEU][hapmap]
rs520500	0.82[ASN][1000 genomes]
rs520629	0.92[CEU][hapmap]
rs537266	0.87[CEU][hapmap]
rs537604	0.87[CEU][hapmap]
rs540063	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap]
rs550404	0.83[CEU][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs556669	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs573766	0.80[CEU][hapmap]
rs578324	0.96[CEU][hapmap]
rs580459	0.83[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap]
rs583122	0.87[CEU][hapmap]
rs588968	0.83[ASN][1000 genomes]
rs589327	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs592712	0.91[CEU][hapmap]
rs597480	0.88[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs609012	0.92[CEU][hapmap]
rs613973	0.92[CEU][hapmap]
rs630613	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631410	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs639688	0.91[CEU][hapmap]
rs641393	0.88[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs644972	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs647175	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs647912	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs650036	0.92[CEU][hapmap]
rs652615	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs653559	0.88[CEU][hapmap]
rs667275	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675513	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs678723	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs679204	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs680498	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs681044	0.92[CEU][hapmap]
rs683105	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs688741	0.92[CEU][hapmap]
rs7103790	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs7123846	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881120	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
8	nsv1047147	chr11:85459235-85594800	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv541114	chr11:85459235-85594800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv2762927	chr11:85468051-85559618	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1052737	chr11:85477084-85554914	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv541115	chr11:85477084-85554914	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1049630	chr11:85486866-85535123	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs556918	SYTL2	cis	multi-tissue	Pritchard
rs556918	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85474000-85487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:85475600-85488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:85480200-85491800	Weak transcription	Gastric	stomach
4	chr11:85483200-85492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:85484200-85488000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:85484200-85488200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:85484400-85488000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:85484400-85488000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:85484400-85488000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:85484400-85488200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:85484600-85487200	Enhancers	Stomach Mucosa	stomach
12	chr11:85484600-85488000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:85484600-85488000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr11:85484600-85488200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:85484600-85488200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:85484600-85488200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:85484600-85490800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:85485200-85487400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr11:85485600-85492800	Weak transcription	Ovary	ovary
20	chr11:85485800-85488200	Weak transcription	Fetal Lung	lung
21	chr11:85486000-85487000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr11:85486000-85488000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:85486000-85488800	Enhancers	Brain Substantia Nigra	brain
24	chr11:85486000-85490800	Weak transcription	NHDF-Ad	bronchial
25	chr11:85486000-85491800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:85486200-85488000	Weak transcription	Fetal Kidney	kidney
27	chr11:85486200-85490800	Weak transcription	NHLF	lung
28	chr11:85486200-85492400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr11:85486400-85487200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr11:85486400-85488200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:85486400-85491000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr11:85486400-85491200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:85486400-85491200	Weak transcription	HSMM	muscle
34	chr11:85486400-85491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr11:85486400-85491800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr11:85486400-85491800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr11:85486400-85491800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr11:85486400-85492600	Weak transcription	Primary T cells from cord blood	blood
39	chr11:85486400-85496200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:85486600-85487000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr11:85486600-85487400	ZNF genes & repeats	Fetal Intestine Small	intestine
42	chr11:85486600-85488000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr11:85486600-85491000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:85486600-85491400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr11:85486600-85491400	Weak transcription	Colonic Mucosa	Colon
46	chr11:85486800-85488000	Weak transcription	Small Intestine	intestine
47	chr11:85486800-85488200	Weak transcription	Fetal Intestine Large	intestine

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