Variant report

Variant	rs290172
Chromosome Location	chr11:85412223-85412224
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:85412022-85412819	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85409414..85413746-chr11:85414065..85417765,4	K562	blood:
2	chr11:85405165..85408368-chr11:85410151..85413068,4	MCF-7	breast:
3	chr11:85406392..85407913-chr11:85410539..85412560,2	K562	blood:

Variant related genes	Relation type
SYTL2	TF binding region
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11234410	0.83[EUR][1000 genomes]
rs188311	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2467059	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs290175	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290177	0.85[ASN][1000 genomes]
rs290178	0.87[ASN][1000 genomes]
rs290186	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs290194	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290196	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290197	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs290199	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs487964	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs489896	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs493673	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs521764	0.82[EUR][1000 genomes]
rs537266	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs558377	0.90[EUR][1000 genomes]
rs56579	0.89[ASN][1000 genomes]
rs573766	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs583122	0.89[EUR][1000 genomes]
rs592380	0.90[EUR][1000 genomes]
rs653559	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv468768	chr11:85395180-85436352	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv555632	chr11:85395180-85436352	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290172	SYTL2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85394000-85427400	Weak transcription	Small Intestine	intestine
2	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
3	chr11:85397000-85412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:85397000-85417400	Weak transcription	Gastric	stomach
5	chr11:85397000-85418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:85397000-85425400	Weak transcription	Lung	lung
7	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
8	chr11:85397600-85422000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:85397600-85428400	Weak transcription	Brain Angular Gyrus	brain
10	chr11:85397800-85412400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:85397800-85421600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:85397800-85430000	Weak transcription	Ovary	ovary
13	chr11:85398000-85427600	Weak transcription	Brain Substantia Nigra	brain
14	chr11:85398400-85413000	Weak transcription	Fetal Stomach	stomach
15	chr11:85405000-85418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:85406200-85429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:85406400-85413800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:85406600-85416000	Weak transcription	A549	lung
19	chr11:85406600-85416800	Weak transcription	NH-A	brain
20	chr11:85406800-85416000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:85407000-85416400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:85407200-85416200	Strong transcription	HSMM	muscle
23	chr11:85407400-85413000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:85408200-85412400	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:85408600-85426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:85409000-85421800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:85409000-85425200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:85409200-85413400	Weak transcription	NHLF	lung
29	chr11:85409400-85418200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:85409400-85427200	Weak transcription	Fetal Lung	lung
31	chr11:85409800-85412400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:85410000-85413000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:85410200-85413000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:85410600-85412600	Enhancers	Fetal Intestine Small	intestine
35	chr11:85410600-85424400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:85411000-85417400	Weak transcription	Fetal Muscle Leg	muscle
37	chr11:85411400-85412800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:85411400-85413000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:85411600-85413000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:85411800-85413000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:85411800-85413200	Weak transcription	NHDF-Ad	bronchial
42	chr11:85411800-85415400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr11:85411800-85424800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr11:85412000-85412800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr11:85412000-85412800	Weak transcription	HSMMtube	muscle
46	chr11:85412000-85415400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr11:85412000-85417400	Weak transcription	Primary T cells from cord blood	blood
48	chr11:85412000-85436800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr11:85412000-85438000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr11:85412200-85414600	Weak transcription	Pancreas	Pancrea

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