Variant report

Variant	rs623120
Chromosome Location	chr11:85487454-85487455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85473245..85476644-chr11:85486524..85489414,3	MCF-7	breast:
2	chr11:85484288..85486316-chr11:85486416..85488624,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10898414	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1893163	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs290193	0.84[EUR][1000 genomes]
rs290198	0.82[EUR][1000 genomes]
rs290201	0.83[EUR][1000 genomes]
rs485485	0.81[ASN][1000 genomes]
rs493078	0.81[ASN][1000 genomes]
rs570394	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs575013	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs652615	0.81[ASN][1000 genomes]
rs667275	0.81[ASN][1000 genomes]
rs683105	0.81[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs623120	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85475600-85488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:85480200-85491800	Weak transcription	Gastric	stomach
3	chr11:85483200-85492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:85484200-85488000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:85484200-85488200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:85484400-85488000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:85484400-85488000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:85484400-85488000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:85484400-85488200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:85484600-85488000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:85484600-85488000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:85484600-85488200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:85484600-85488200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:85484600-85488200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:85484600-85490800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:85485600-85492800	Weak transcription	Ovary	ovary
17	chr11:85485800-85488200	Weak transcription	Fetal Lung	lung
18	chr11:85486000-85488000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:85486000-85488800	Enhancers	Brain Substantia Nigra	brain
20	chr11:85486000-85490800	Weak transcription	NHDF-Ad	bronchial
21	chr11:85486000-85491800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:85486200-85488000	Weak transcription	Fetal Kidney	kidney
23	chr11:85486200-85490800	Weak transcription	NHLF	lung
24	chr11:85486200-85492400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr11:85486400-85488200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:85486400-85491000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:85486400-85491200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:85486400-85491200	Weak transcription	HSMM	muscle
29	chr11:85486400-85491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:85486400-85491800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:85486400-85491800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:85486400-85491800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:85486400-85492600	Weak transcription	Primary T cells from cord blood	blood
34	chr11:85486400-85496200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:85486600-85488000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr11:85486600-85491000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:85486600-85491400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:85486600-85491400	Weak transcription	Colonic Mucosa	Colon
39	chr11:85486800-85488000	Weak transcription	Small Intestine	intestine
40	chr11:85486800-85488200	Weak transcription	Fetal Intestine Large	intestine
41	chr11:85487000-85488000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr11:85487000-85488600	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr11:85487200-85487800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr11:85487200-85488200	Weak transcription	Stomach Mucosa	stomach
45	chr11:85487200-85488600	Enhancers	Brain Cingulate Gyrus	brain
46	chr11:85487200-85488600	Enhancers	Brain Hippocampus Middle	brain
47	chr11:85487400-85488000	Weak transcription	Fetal Intestine Small	intestine
48	chr11:85487400-85488200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:85487400-85488800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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