Variant report

Variant	rs2166519
Chromosome Location	chr11:18650393-18650394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18646819..18652740-chr11:18653363..18657405,11	K562	blood:
2	chr11:18635938..18638203-chr11:18650353..18652187,2	MCF-7	breast:
3	chr11:18649875..18652802-chr11:18653746..18657273,3	MCF-7	breast:
4	chr11:18647229..18652774-chr11:18654335..18657734,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179119	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10128711	0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs10500834	0.91[YRI][hapmap]
rs10734261	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832948	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832949	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832956	0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs10832957	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10832962	0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs11024737	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024739	0.88[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs11024745	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605097	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11607095	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12365747	0.91[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2403321	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4373895	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757678	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934205	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7943121	1.00[YRI][hapmap]
rs7943131	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2166519	PRMT3	cis	cerebellum	SCAN
rs2166519	SAAL1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18629000-18654400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:18630800-18654800	Weak transcription	Psoas Muscle	Psoas
3	chr11:18637000-18655200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:18637400-18654400	Weak transcription	Brain Angular Gyrus	brain
5	chr11:18637400-18654400	Weak transcription	Fetal Intestine Small	intestine
6	chr11:18637400-18654800	Weak transcription	Esophagus	oesophagus
7	chr11:18637400-18654800	Weak transcription	Lung	lung
8	chr11:18637400-18654800	Weak transcription	Pancreas	Pancrea
9	chr11:18637600-18650600	Weak transcription	Gastric	stomach
10	chr11:18637600-18654000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:18637600-18654200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:18637600-18654200	Weak transcription	Hela-S3	cervix
13	chr11:18637600-18654400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:18637600-18654400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:18637600-18654400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:18637600-18654800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:18637600-18654800	Weak transcription	Right Ventricle	heart
18	chr11:18637600-18654800	Weak transcription	Spleen	Spleen
19	chr11:18637800-18654800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:18637800-18654800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:18637800-18654800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:18638000-18654400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:18638000-18654400	Weak transcription	Fetal Intestine Large	intestine
24	chr11:18638000-18654600	Weak transcription	Brain Substantia Nigra	brain
25	chr11:18638200-18654800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:18638400-18654400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr11:18638400-18654400	Weak transcription	K562	blood
28	chr11:18638400-18654800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr11:18640200-18654600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr11:18640400-18654200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:18640400-18654200	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:18640400-18654400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:18640400-18654400	Weak transcription	HepG2	liver
34	chr11:18640400-18654800	Weak transcription	Aorta	Aorta
35	chr11:18640600-18654200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:18640600-18654200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:18640600-18654400	Weak transcription	A549	lung
38	chr11:18640600-18654400	Weak transcription	NH-A	brain
39	chr11:18640600-18654600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr11:18640600-18654800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:18640600-18654800	Weak transcription	Thymus	Thymus
42	chr11:18640800-18654200	Weak transcription	NHEK	skin
43	chr11:18640800-18654800	Weak transcription	HSMM	muscle
44	chr11:18641000-18654200	Weak transcription	Liver	Liver
45	chr11:18641000-18654200	Weak transcription	Osteobl	bone
46	chr11:18641000-18654400	Weak transcription	Fetal Lung	lung
47	chr11:18641000-18654400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:18641000-18654800	Weak transcription	Small Intestine	intestine
49	chr11:18641000-18654800	Weak transcription	Stomach Mucosa	stomach
50	chr11:18641200-18654800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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