Variant report

Variant	rs290190
Chromosome Location	chr11:85427450-85427451
allele	A/G
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	SP1	chr11:85427151-85427774	A549	lung:	n/a	chr11:85427314-85427321
2	SP1	chr11:85427169-85427682	A549	lung:	n/a	chr11:85427314-85427321

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC89-4	chr11:85427386-85427474	NONHSAT023446
2	lnc-CCDC89-4	chr11:85427324-85427471	NONHSAT023447

Variant related genes	Relation type
SYTL2	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1046216	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11603256	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11606656	0.81[CHB][hapmap]
rs1237203	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1445497	0.81[CHB][hapmap]
rs188311	0.87[CEU][hapmap]
rs2196168	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs290173	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290174	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290175	0.88[CEU][hapmap]
rs290183	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs290184	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs290185	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs290191	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290193	0.87[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs290194	0.84[CEU][hapmap]
rs290195	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290196	0.88[CEU][hapmap]
rs290198	0.80[ASN][1000 genomes]
rs290199	0.84[CEU][hapmap]
rs290200	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290201	0.85[ASN][1000 genomes]
rs290202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370385	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3753050	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3781815	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3824956	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3862782	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs475491	0.90[EUR][1000 genomes]
rs478089	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs485485	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs491867	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs493078	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4944538	0.82[CHB][hapmap];0.81[YRI][hapmap]
rs496187	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs510948	0.87[CEU][hapmap]
rs520629	0.83[CEU][hapmap]
rs537266	0.87[CEU][hapmap]
rs537604	0.87[CEU][hapmap]
rs540063	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs550404	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs556669	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs556918	0.84[EUR][1000 genomes]
rs56579	0.85[YRI][hapmap]
rs575013	0.81[JPT][hapmap]
rs578324	0.87[CEU][hapmap]
rs580459	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs588968	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs589327	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs592460	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs592712	0.91[CEU][hapmap]
rs594892	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs597480	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs609012	0.83[CEU][hapmap]
rs613973	0.84[CEU][hapmap]
rs631410	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs639688	0.83[CEU][hapmap]
rs641393	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs644972	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs647175	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs647912	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs650036	0.83[CEU][hapmap]
rs675513	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs678376	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs678723	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs679204	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs680498	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs681044	0.84[CEU][hapmap]
rs683105	0.80[EUR][1000 genomes]
rs688741	0.83[CEU][hapmap]
rs7103790	0.81[CHB][hapmap]
rs7107788	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7116195	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7123846	0.82[AMR][1000 genomes]
rs881120	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs956202	0.91[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290190	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
2	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
3	chr11:85397600-85428400	Weak transcription	Brain Angular Gyrus	brain
4	chr11:85397800-85430000	Weak transcription	Ovary	ovary
5	chr11:85398000-85427600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:85406200-85429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:85412000-85436800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:85412000-85438000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:85413600-85429600	Weak transcription	Fetal Stomach	stomach
10	chr11:85413800-85430000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:85417600-85428600	Weak transcription	Osteobl	bone
12	chr11:85417600-85453000	Weak transcription	Gastric	stomach
13	chr11:85418400-85436400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:85422400-85427800	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:85422400-85428000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:85422400-85430200	Weak transcription	Fetal Kidney	kidney
17	chr11:85422600-85428600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr11:85422600-85448600	Weak transcription	Fetal Intestine Large	intestine
19	chr11:85422800-85448200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr11:85423000-85429800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:85423600-85430000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:85424000-85448600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:85424200-85427800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:85424400-85428400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:85424600-85429800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:85425200-85428600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:85425400-85428600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:85425600-85429600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:85425600-85429800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:85425800-85429600	Weak transcription	Primary T cells from cord blood	blood
31	chr11:85425800-85429600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:85426600-85427600	Flanking Active TSS	NHDF-Ad	bronchial
33	chr11:85426600-85428600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr11:85426800-85428200	Flanking Active TSS	A549	lung
35	chr11:85427000-85428000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr11:85427000-85428000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:85427000-85428200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:85427000-85428200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr11:85427000-85428400	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr11:85427000-85428800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr11:85427000-85430600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr11:85427200-85427600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr11:85427200-85427600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr11:85427200-85427800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr11:85427200-85427800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:85427200-85428000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:85427200-85428000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr11:85427200-85428600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr11:85427200-85428800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:85427200-85429600	Active TSS	Fetal Muscle Leg	muscle

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