Variant report

Variant	rs6578423
Chromosome Location	chr11:3969444-3969445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10430939	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10458900	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs10500591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10500592	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap]
rs11030251	0.96[ASN][1000 genomes]
rs11030286	0.96[ASN][1000 genomes]
rs11030326	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.99[ASN][1000 genomes]
rs11030327	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11030366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11030417	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11030418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11030478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs11030479	0.97[ASN][1000 genomes]
rs11030481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs11030484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs11030485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs11030486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[ASN][1000 genomes]
rs11030697	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs11030796	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs11525342	0.87[ASN][1000 genomes]
rs11529865	0.87[ASN][1000 genomes]
rs11827795	0.88[YRI][hapmap]
rs12222250	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12224469	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1372803	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs16929410	0.81[CHB][hapmap]
rs16929438	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs16929467	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs16929477	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs16929480	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs16929488	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs16929492	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs16929529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs16929531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs16929538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs16929540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs16929542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs16929546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs16929611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16929616	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[ASN][1000 genomes]
rs16929653	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1822286	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs1899478	0.82[ASN][1000 genomes]
rs2167562	0.89[YRI][hapmap]
rs2167563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750994	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs4910878	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs55679086	0.97[ASN][1000 genomes]
rs55978228	0.97[ASN][1000 genomes]
rs56126231	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56140937	0.81[ASN][1000 genomes]
rs59195871	0.91[ASN][1000 genomes]
rs59242983	0.83[ASN][1000 genomes]
rs60930198	0.87[ASN][1000 genomes]
rs61897162	0.95[ASN][1000 genomes]
rs61897163	0.96[ASN][1000 genomes]
rs61897164	0.96[ASN][1000 genomes]
rs61897166	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897167	0.95[ASN][1000 genomes]
rs61897170	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897171	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897194	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897195	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61897201	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61897202	0.97[ASN][1000 genomes]
rs61897203	0.84[ASN][1000 genomes]
rs61897234	0.86[ASN][1000 genomes]
rs61897237	0.85[ASN][1000 genomes]
rs61897238	0.83[ASN][1000 genomes]
rs61897254	0.81[ASN][1000 genomes]
rs6578435	0.89[YRI][hapmap]
rs723779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72847181	0.80[ASN][1000 genomes]
rs72851736	0.97[ASN][1000 genomes]
rs750526	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7924332	0.89[YRI][hapmap]
rs7928117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs7934581	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs7938706	0.89[YRI][hapmap]
rs7939086	0.88[YRI][hapmap]
rs7941743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894454	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs894456	0.84[YRI][hapmap]

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	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv896895	chr11:3942001-3972236	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6578423	LRTM1	trans	brain	seeQTL
rs6578423	GUCA1C	trans	brain	seeQTL
rs6578423	TTR	trans	brain	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3950400-3972200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:3961600-3975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:3962000-3971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:3962000-3973400	Weak transcription	Ovary	ovary
6	chr11:3963000-3973200	Enhancers	Primary B cells from peripheral blood	blood
7	chr11:3964400-3971600	Weak transcription	A549	lung
8	chr11:3964400-3972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:3964400-3972400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:3964600-3970000	Weak transcription	K562	blood
11	chr11:3965400-3970200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:3965800-3970400	Enhancers	Colon Smooth Muscle	Colon
13	chr11:3965800-3972000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:3966000-3972200	Weak transcription	Pancreas	Pancrea
15	chr11:3967000-3972600	Weak transcription	Fetal Intestine Small	intestine
16	chr11:3967200-3969600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr11:3967200-3970800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:3967400-3971200	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr11:3967400-3971400	Enhancers	Fetal Heart	heart
20	chr11:3967600-3969600	Enhancers	Fetal Lung	lung
21	chr11:3967800-3969600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr11:3967800-3971200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:3968000-3972200	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:3968200-3971000	Active TSS	Thymus	Thymus
25	chr11:3968200-3972000	Weak transcription	Stomach Mucosa	stomach
26	chr11:3968200-3974600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr11:3968200-3980200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:3968400-3969600	Flanking Active TSS	Fetal Thymus	thymus
29	chr11:3968600-3969600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr11:3968600-3970400	Enhancers	Primary hematopoietic stem cells	blood
31	chr11:3968600-3971200	Flanking Active TSS	Dnd41	blood
32	chr11:3968600-3971800	Weak transcription	Osteobl	bone
33	chr11:3968600-3972200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:3968600-3972200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:3968600-3972200	Weak transcription	Brain Angular Gyrus	brain
36	chr11:3968800-3969800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:3968800-3972000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:3968800-3974600	Weak transcription	HMEC	breast
39	chr11:3969000-3969600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:3969000-3970000	Enhancers	GM12878-XiMat	blood
41	chr11:3969000-3970200	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr11:3969000-3970200	Weak transcription	HSMM	muscle
43	chr11:3969000-3970600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:3969000-3970600	Weak transcription	Small Intestine	intestine
45	chr11:3969000-3971400	Weak transcription	Spleen	Spleen
46	chr11:3969000-3971600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:3969000-3971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:3969000-3971800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:3969000-3971800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:3969000-3972000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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