Variant report

Variant	rs290179
Chromosome Location	chr11:85400063-85400064
allele	C/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	chr11:85400025-85400133	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85372316..85374513-chr11:85398515..85401514,2	K562	blood:

Variant related genes	Relation type
CCDC89	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11603256	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1237203	0.81[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs2117312	0.82[ASN][1000 genomes]
rs2196168	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs290171	0.86[CHB][hapmap]
rs290180	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs290181	0.83[ASN][1000 genomes]
rs290183	0.87[CHB][hapmap]
rs290184	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs290185	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs290193	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs290198	0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs290201	0.89[ASN][1000 genomes]
rs370385	0.82[CHB][hapmap]
rs3753050	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs3781815	0.81[CHB][hapmap]
rs3824956	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs3862782	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs431606	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs575013	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs575050	0.81[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs592460	0.82[CHB][hapmap]
rs7107788	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs7116195	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs881120	0.82[CHB][hapmap]
rs956202	0.82[CHB][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290179	GRM5	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85394000-85427400	Weak transcription	Small Intestine	intestine
2	chr11:85394200-85401800	Weak transcription	Primary T cells from cord blood	blood
3	chr11:85394200-85404200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:85394200-85406200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr11:85394200-85410600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:85394200-85410800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:85394400-85410400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:85394400-85410600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
10	chr11:85397000-85412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:85397000-85417400	Weak transcription	Gastric	stomach
12	chr11:85397000-85418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:85397000-85425400	Weak transcription	Lung	lung
14	chr11:85397200-85400400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr11:85397200-85401200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:85397200-85405800	Weak transcription	Aorta	Aorta
17	chr11:85397200-85406000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:85397200-85406400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:85397200-85409200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:85397200-85409200	Weak transcription	Placenta	Placenta
21	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
22	chr11:85397400-85401600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr11:85397400-85410400	Weak transcription	Left Ventricle	heart
24	chr11:85397600-85402800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:85397600-85404000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:85397600-85406200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:85397600-85407200	Weak transcription	Fetal Kidney	kidney
28	chr11:85397600-85409800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:85397600-85422000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:85397600-85428400	Weak transcription	Brain Angular Gyrus	brain
31	chr11:85397800-85401800	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:85397800-85403200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:85397800-85406000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:85397800-85407200	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:85397800-85407800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:85397800-85410600	Weak transcription	Fetal Intestine Small	intestine
37	chr11:85397800-85412400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr11:85397800-85421600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr11:85397800-85430000	Weak transcription	Ovary	ovary
40	chr11:85398000-85402800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:85398000-85408600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:85398000-85427600	Weak transcription	Brain Substantia Nigra	brain
43	chr11:85398200-85404200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:85398400-85400400	Weak transcription	HSMMtube	muscle
45	chr11:85398400-85401000	Weak transcription	HSMM	muscle
46	chr11:85398400-85401400	Weak transcription	NHLF	lung
47	chr11:85398400-85405800	Weak transcription	Fetal Lung	lung
48	chr11:85398400-85413000	Weak transcription	Fetal Stomach	stomach
49	chr11:85398600-85401000	Weak transcription	NHDF-Ad	bronchial
50	chr11:85400000-85405800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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