Variant report

Variant	rs56579
Chromosome Location	chr11:85404138-85404139
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	chr11:85374882..85377605-chr11:85402891..85406300,3	MCF-7	breast:
2	chr11:85403066..85404885-chr11:85408598..85410390,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137504	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10501595	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11234359	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs11604141	0.81[JPT][hapmap]
rs11820071	0.82[ASN][1000 genomes]
rs1192	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1214001	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12417341	0.86[ASN][1000 genomes]
rs12419172	0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1354397	0.95[CHB][hapmap]
rs1445513	0.81[JPT][hapmap]
rs17148254	0.86[ASN][1000 genomes]
rs17148293	0.88[ASN][1000 genomes]
rs17148306	0.87[ASN][1000 genomes]
rs17208492	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs17208519	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs17810659	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs188311	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1892872	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1991923	0.90[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2162055	0.81[ASN][1000 genomes]
rs2290823	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2467059	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs290172	0.89[ASN][1000 genomes]
rs290173	0.85[YRI][hapmap]
rs290175	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs290177	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290178	0.97[ASN][1000 genomes]
rs290182	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs290186	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]
rs290190	0.85[YRI][hapmap]
rs290194	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs290196	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs290197	0.83[ASN][1000 genomes]
rs290199	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs290200	0.85[YRI][hapmap]
rs290202	0.85[YRI][hapmap]
rs35844123	0.86[ASN][1000 genomes]
rs487964	0.80[ASN][1000 genomes]
rs4943925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4944527	0.84[ASN][1000 genomes]
rs4944529	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4944531	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4944532	0.87[ASN][1000 genomes]
rs497698	0.81[ASN][1000 genomes]
rs510948	0.94[JPT][hapmap]
rs520629	0.81[JPT][hapmap]
rs537266	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs537604	0.94[JPT][hapmap]
rs573766	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs578324	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs58152312	0.86[ASN][1000 genomes]
rs583122	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs58931064	0.86[ASN][1000 genomes]
rs592712	0.94[JPT][hapmap]
rs609012	0.94[JPT][hapmap]
rs613973	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs639688	0.88[JPT][hapmap]
rs650036	1.00[JPT][hapmap]
rs653559	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs6592252	0.82[ASN][1000 genomes]
rs6592253	0.82[ASN][1000 genomes]
rs678376	0.85[YRI][hapmap]
rs681044	0.94[JPT][hapmap]
rs688741	1.00[JPT][hapmap]
rs7108132	0.82[ASN][1000 genomes]
rs7115250	0.84[ASN][1000 genomes]
rs7119617	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs7943586	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7948778	1.00[CHB][hapmap]
rs881121	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs947861	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs947862	0.86[ASN][1000 genomes]
rs947863	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.86[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
rs56579	ME3	cis	cerebellum	SCAN
rs56579	GRM5	cis	parietal	SCAN
rs56579	SYTL2	cis	Muscle Skeletal	GTEx
rs56579	SYTL2	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85394000-85427400	Weak transcription	Small Intestine	intestine
2	chr11:85394200-85404200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:85394200-85406200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:85394200-85410600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr11:85394200-85410800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:85394400-85410400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:85394400-85410600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
9	chr11:85397000-85412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:85397000-85417400	Weak transcription	Gastric	stomach
11	chr11:85397000-85418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:85397000-85425400	Weak transcription	Lung	lung
13	chr11:85397200-85405800	Weak transcription	Aorta	Aorta
14	chr11:85397200-85406000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:85397200-85406400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:85397200-85409200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:85397200-85409200	Weak transcription	Placenta	Placenta
18	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
19	chr11:85397400-85410400	Weak transcription	Left Ventricle	heart
20	chr11:85397600-85406200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:85397600-85407200	Weak transcription	Fetal Kidney	kidney
22	chr11:85397600-85409800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:85397600-85422000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr11:85397600-85428400	Weak transcription	Brain Angular Gyrus	brain
25	chr11:85397800-85406000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:85397800-85407200	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:85397800-85407800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:85397800-85410600	Weak transcription	Fetal Intestine Small	intestine
29	chr11:85397800-85412400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:85397800-85421600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:85397800-85430000	Weak transcription	Ovary	ovary
32	chr11:85398000-85408600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:85398000-85427600	Weak transcription	Brain Substantia Nigra	brain
34	chr11:85398200-85404200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:85398400-85405800	Weak transcription	Fetal Lung	lung
36	chr11:85398400-85413000	Weak transcription	Fetal Stomach	stomach
37	chr11:85400000-85405800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:85400000-85410600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:85400400-85409200	Strong transcription	HSMMtube	muscle
40	chr11:85400400-85411400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr11:85401000-85405400	Strong transcription	NHDF-Ad	bronchial
42	chr11:85401000-85406000	Strong transcription	HSMM	muscle
43	chr11:85401200-85410600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr11:85401400-85405600	Strong transcription	NHLF	lung
45	chr11:85401600-85407600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr11:85401800-85405000	Strong transcription	Primary T cells from cord blood	blood
47	chr11:85401800-85407600	Strong transcription	Fetal Muscle Leg	muscle
48	chr11:85402000-85410400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr11:85402800-85404600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:85402800-85405600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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