Variant report

Variant	rs290173
Chromosome Location	chr11:85408832-85408833
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	chr11:85403066..85404885-chr11:85408598..85410390,2	MCF-7	breast:
2	chr11:85407594..85410052-chr11:85416744..85418480,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1046216	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10898410	0.80[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs11603256	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs11606656	0.87[CHD][hapmap]
rs1237203	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs1445497	0.87[CHD][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap]
rs188311	0.81[CEU][hapmap]
rs1893163	0.81[LWK][hapmap]
rs2196168	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2374683	0.80[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs290174	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290175	0.81[CEU][hapmap]
rs290183	0.87[CHB][hapmap]
rs290184	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs290185	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs290190	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]
rs290191	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290193	0.88[ASW][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs290195	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290196	0.80[CEU][hapmap]
rs290198	0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs290200	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290201	0.80[ASN][1000 genomes]
rs290202	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs370385	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3753050	0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3781815	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs3817087	0.80[ASN][1000 genomes]
rs3824956	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3862782	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs475491	0.90[EUR][1000 genomes]
rs478089	0.91[EUR][1000 genomes]
rs485485	0.85[EUR][1000 genomes]
rs491867	0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs493078	0.84[EUR][1000 genomes]
rs4944530	0.80[ASN][1000 genomes]
rs4944538	0.85[YRI][hapmap]
rs496187	0.81[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs510948	0.81[CEU][hapmap]
rs537266	0.80[CEU][hapmap]
rs537604	0.81[CEU][hapmap]
rs540063	0.81[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs550404	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs556669	0.84[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs556918	0.83[EUR][1000 genomes]
rs56579	0.85[YRI][hapmap]
rs575013	0.90[CHD][hapmap];0.88[LWK][hapmap]
rs578324	0.80[CEU][hapmap]
rs580459	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs588968	0.82[EUR][1000 genomes]
rs589327	0.84[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs592460	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs592712	0.84[CEU][hapmap]
rs594892	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs597480	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs631410	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs641393	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs644972	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs647175	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs647912	0.81[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs675513	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs678376	0.94[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs678723	0.92[EUR][1000 genomes]
rs679204	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs680498	0.81[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap]
rs7103790	0.87[CHD][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap]
rs7107788	0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7116195	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs881120	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs956202	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs290173	GRM5	cis	parietal	SCAN
rs290173	ME3	cis	cerebellum	SCAN
rs290173	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85394000-85427400	Weak transcription	Small Intestine	intestine
2	chr11:85394200-85410600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr11:85394200-85410800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:85394400-85410400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:85394400-85410600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
7	chr11:85397000-85412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:85397000-85417400	Weak transcription	Gastric	stomach
9	chr11:85397000-85418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:85397000-85425400	Weak transcription	Lung	lung
11	chr11:85397200-85409200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:85397200-85409200	Weak transcription	Placenta	Placenta
13	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
14	chr11:85397400-85410400	Weak transcription	Left Ventricle	heart
15	chr11:85397600-85409800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:85397600-85422000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:85397600-85428400	Weak transcription	Brain Angular Gyrus	brain
18	chr11:85397800-85410600	Weak transcription	Fetal Intestine Small	intestine
19	chr11:85397800-85412400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:85397800-85421600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:85397800-85430000	Weak transcription	Ovary	ovary
22	chr11:85398000-85427600	Weak transcription	Brain Substantia Nigra	brain
23	chr11:85398400-85413000	Weak transcription	Fetal Stomach	stomach
24	chr11:85400000-85410600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:85400400-85409200	Strong transcription	HSMMtube	muscle
26	chr11:85400400-85411400	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr11:85401200-85410600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr11:85402000-85410400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr11:85404800-85410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:85405000-85418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:85406000-85409000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:85406000-85410000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:85406000-85410400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr11:85406000-85410600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr11:85406200-85409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:85406200-85410400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:85406200-85429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:85406400-85409000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:85406400-85409400	Strong transcription	Primary T cells from cord blood	blood
40	chr11:85406400-85413800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:85406600-85410400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:85406600-85416000	Weak transcription	A549	lung
43	chr11:85406600-85416800	Weak transcription	NH-A	brain
44	chr11:85406800-85416000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:85407000-85410200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:85407000-85416400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:85407200-85409000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:85407200-85416200	Strong transcription	HSMM	muscle
49	chr11:85407400-85409000	Weak transcription	Osteobl	bone
50	chr11:85407400-85409200	Strong transcription	NHLF	lung

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