Variant report

Variant	rs1445497
Chromosome Location	chr11:85518585-85518586
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85497196..85498847-chr11:85516352..85520145,3	MCF-7	breast:
2	chr11:85374332..85377604-chr11:85518032..85524824,7	MCF-7	breast:
3	chr11:85433923..85435734-chr11:85518099..85520604,2	MCF-7	breast:
4	chr11:85494490..85496333-chr11:85515737..85519342,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137504	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10898406	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898410	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10898413	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898414	0.88[ASN][1000 genomes]
rs10898415	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11604141	0.86[CEU][hapmap]
rs11606656	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12362853	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1445513	0.82[CEU][hapmap]
rs1481700	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1893163	0.83[ASW][hapmap];0.84[CHD][hapmap];0.95[LWK][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2008890	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2044391	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2044392	0.92[ASN][1000 genomes]
rs2374683	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs290173	0.87[CHD][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap]
rs290190	0.81[CHB][hapmap]
rs290195	0.81[CHB][hapmap];0.85[YRI][hapmap]
rs290200	0.83[CHD][hapmap]
rs290202	0.81[CHB][hapmap];0.85[CHD][hapmap];0.96[MEX][hapmap]
rs475380	0.82[ASN][1000 genomes]
rs478089	0.84[ASN][1000 genomes]
rs485485	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491867	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs493078	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4944538	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs496187	0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs520500	0.80[ASN][1000 genomes]
rs540063	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs556918	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs575013	0.83[CHD][hapmap];0.92[LWK][hapmap];0.85[YRI][hapmap]
rs588968	0.82[ASN][1000 genomes]
rs589327	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs597480	0.90[LWK][hapmap];0.96[MEX][hapmap];0.92[YRI][hapmap]
rs630613	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs631410	0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs641393	0.90[LWK][hapmap];0.96[MEX][hapmap];0.92[YRI][hapmap]
rs644972	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs647912	0.91[CHB][hapmap];0.90[CHD][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs652615	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs667275	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs678723	0.84[ASN][1000 genomes]
rs679204	0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs680498	0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs683105	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7103790	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123846	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	nsv1047147	chr11:85459235-85594800	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv541114	chr11:85459235-85594800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv2762927	chr11:85468051-85559618	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1052737	chr11:85477084-85554914	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv541115	chr11:85477084-85554914	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1049630	chr11:85486866-85535123	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1445497	GRM5	cis	parietal	SCAN
rs1445497	SYTL2	cis	Nerve Tibial	GTEx
rs1445497	SYTL2	cis	multi-tissue	Pritchard
rs1445497	SYTL2	cis	cerebellum	SCAN
rs1445497	SYTL2	cis	Muscle Skeletal	GTEx
rs1445497	ME3	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85509800-85520000	Weak transcription	HSMM	muscle
2	chr11:85510800-85520200	Weak transcription	Fetal Muscle Leg	muscle
3	chr11:85512000-85520000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:85514000-85520000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:85514000-85520200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:85514600-85520200	Weak transcription	Gastric	stomach
7	chr11:85515000-85520000	Weak transcription	Primary T cells from cord blood	blood
8	chr11:85515000-85520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:85515000-85520400	Weak transcription	Fetal Brain Male	brain
10	chr11:85516000-85521000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:85516200-85518800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:85516200-85519000	Enhancers	HMEC	breast
13	chr11:85516400-85518600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:85516400-85518800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:85516600-85519000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:85516600-85520800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr11:85516800-85519000	Enhancers	NHEK	skin
18	chr11:85516800-85520200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:85517000-85520000	Weak transcription	Fetal Stomach	stomach
20	chr11:85517000-85520200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:85517200-85518800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:85517800-85518600	Enhancers	Stomach Mucosa	stomach
23	chr11:85518000-85518800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr11:85518000-85518800	Enhancers	Brain Cingulate Gyrus	brain
25	chr11:85518000-85519600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr11:85518200-85518600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr11:85518200-85518600	Weak transcription	Small Intestine	intestine
28	chr11:85518200-85519600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:85518200-85519800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:85518200-85519800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:85518200-85520000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:85518200-85520000	Weak transcription	Psoas Muscle	Psoas
33	chr11:85518200-85520000	Weak transcription	NHLF	lung
34	chr11:85518200-85520200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr11:85518200-85520400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:85518200-85520800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:85518200-85520800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:85518200-85520800	Weak transcription	Esophagus	oesophagus
39	chr11:85518200-85521000	Weak transcription	Right Atrium	heart
40	chr11:85518200-85521200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:85518400-85519000	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr11:85518400-85520000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:85518400-85520000	Weak transcription	Brain Angular Gyrus	brain
44	chr11:85518400-85520000	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:85518400-85520000	Weak transcription	NHDF-Ad	bronchial
46	chr11:85518400-85520200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr11:85518400-85520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:85518400-85520800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:85518400-85520800	Weak transcription	Brain Substantia Nigra	brain

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