Variant report

Variant	rs290186
Chromosome Location	chr11:85395652-85395653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:85392491-85397452	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85387868..85389432-chr11:85395056..85397188,2	MCF-7	breast:
2	chr11:85337931..85339718-chr11:85394952..85396893,2	K562	blood:
3	chr11:85374139..85377473-chr11:85394538..85397297,3	MCF-7	breast:
4	chr11:85375817..85377426-chr11:85394328..85396398,2	K562	blood:
5	chr11:85394543..85396055-chr11:85509684..85512654,2	MCF-7	breast:
6	chr11:85389569..85392078-chr11:85394347..85396779,2	MCF-7	breast:

No data

Variant related genes	Relation type
CREBZF	TF binding region
ENSG00000171204	Chromatin interaction
ENSG00000137504	Chromatin interaction
ENSG00000150672	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10501595	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11234359	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs11604028	0.81[ASN][1000 genomes]
rs11604141	0.81[JPT][hapmap]
rs11820071	0.85[ASN][1000 genomes]
rs1192	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.80[MKK][hapmap];0.93[ASN][1000 genomes]
rs1214001	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.80[MKK][hapmap];0.89[ASN][1000 genomes]
rs12417341	0.93[ASN][1000 genomes]
rs12419172	0.91[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.84[ASN][1000 genomes]
rs1354397	0.95[CHB][hapmap]
rs1445513	0.81[JPT][hapmap]
rs17148254	0.92[ASN][1000 genomes]
rs17148293	0.91[ASN][1000 genomes]
rs17148306	0.90[ASN][1000 genomes]
rs17208492	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17208519	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17810659	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs188311	0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1892872	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1991923	0.90[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2162055	0.87[ASN][1000 genomes]
rs2290823	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2467059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290172	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs290175	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs290177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs290178	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs290182	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs290194	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs290196	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs290199	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs35844123	0.92[ASN][1000 genomes]
rs489896	0.81[AMR][1000 genomes]
rs4943925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4944527	0.90[ASN][1000 genomes]
rs4944529	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4944531	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4944532	0.90[ASN][1000 genomes]
rs497698	0.86[ASN][1000 genomes]
rs510948	0.94[JPT][hapmap]
rs520629	0.81[JPT][hapmap]
rs537266	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs537604	0.94[JPT][hapmap]
rs56073783	0.82[ASN][1000 genomes]
rs56579	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs57223077	0.82[ASN][1000 genomes]
rs573766	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs578324	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs58152312	0.92[ASN][1000 genomes]
rs583122	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs58931064	0.92[ASN][1000 genomes]
rs592712	0.94[JPT][hapmap]
rs60838923	0.85[ASN][1000 genomes]
rs609012	0.94[JPT][hapmap]
rs61286868	0.81[ASN][1000 genomes]
rs613973	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs639688	0.88[JPT][hapmap]
rs650036	1.00[JPT][hapmap]
rs653559	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs6592252	0.89[ASN][1000 genomes]
rs6592253	0.89[ASN][1000 genomes]
rs681044	0.94[JPT][hapmap]
rs688741	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7108132	0.89[ASN][1000 genomes]
rs7108137	0.82[ASN][1000 genomes]
rs7115250	0.90[ASN][1000 genomes]
rs7119617	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs7939217	0.85[ASN][1000 genomes]
rs7943586	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7948778	1.00[CHB][hapmap]
rs881121	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs947861	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs947862	0.92[ASN][1000 genomes]
rs947863	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs290186	GRM5	cis	parietal	SCAN
rs290186	CCDC89	cis	cerebellum	SCAN
rs290186	SYTL2	cis	lymphoblastoid	seeQTL
rs290186	RAB38	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85392400-85396200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:85392400-85396200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:85394000-85396200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:85394000-85427400	Weak transcription	Small Intestine	intestine
5	chr11:85394200-85395800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:85394200-85395800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:85394200-85395800	Weak transcription	Brain Angular Gyrus	brain
8	chr11:85394200-85395800	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:85394200-85395800	Weak transcription	Fetal Heart	heart
10	chr11:85394200-85395800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:85394200-85396000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:85394200-85396000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:85394200-85396000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:85394200-85396000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:85394200-85396000	Weak transcription	Adipose Nuclei	Adipose
16	chr11:85394200-85396000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:85394200-85396000	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:85394200-85396000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:85394200-85396000	Weak transcription	Brain Substantia Nigra	brain
20	chr11:85394200-85396000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:85394200-85396000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:85394200-85396000	Weak transcription	Placenta	Placenta
23	chr11:85394200-85396000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:85394200-85396000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr11:85394200-85396000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:85394200-85396000	Weak transcription	Stomach Mucosa	stomach
27	chr11:85394200-85396000	Weak transcription	Spleen	Spleen
28	chr11:85394200-85396000	Weak transcription	NH-A	brain
29	chr11:85394200-85396200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:85394200-85396200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:85394200-85396200	Weak transcription	Gastric	stomach
32	chr11:85394200-85396200	Weak transcription	Left Ventricle	heart
33	chr11:85394200-85396200	Weak transcription	Lung	lung
34	chr11:85394200-85396200	Weak transcription	Psoas Muscle	Psoas
35	chr11:85394200-85396200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:85394200-85396400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:85394200-85396400	Weak transcription	Fetal Brain Male	brain
38	chr11:85394200-85396400	Weak transcription	Fetal Thymus	thymus
39	chr11:85394200-85396400	Weak transcription	NHEK	skin
40	chr11:85394200-85396800	Weak transcription	Esophagus	oesophagus
41	chr11:85394200-85396800	Weak transcription	Fetal Brain Female	brain
42	chr11:85394200-85396800	Weak transcription	Thymus	Thymus
43	chr11:85394200-85401800	Weak transcription	Primary T cells from cord blood	blood
44	chr11:85394200-85404200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:85394200-85406200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:85394200-85410600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr11:85394200-85410800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:85394400-85395800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:85394400-85395800	Weak transcription	Fetal Intestine Large	intestine
50	chr11:85394400-85395800	Weak transcription	Fetal Kidney	kidney

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