Variant report

Variant	rs11155475
Chromosome Location	chr6:146872685-146872686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12189826	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804286	0.95[CEU][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes]
rs3804288	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs3804289	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6570768	0.95[CEU][hapmap]
rs6915731	0.95[CEU][hapmap]
rs6918907	0.81[EUR][1000 genomes]
rs6939108	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs7773384	0.92[EUR][1000 genomes]
rs9373498	0.94[EUR][1000 genomes]
rs9377003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9377004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390393	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399580	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033913	chr6:146572989-147092365	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538466	chr6:146572989-147092365	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv886749	chr6:146679735-147123699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11155475	STX11	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146865800-146877400	Weak transcription	Placenta	Placenta
2	chr6:146865800-146878200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:146866400-146881800	Weak transcription	Brain Germinal Matrix	brain
4	chr6:146866600-146875800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:146866600-146876200	Weak transcription	Psoas Muscle	Psoas
6	chr6:146866600-146877800	Weak transcription	Gastric	stomach
7	chr6:146866600-146877800	Weak transcription	Lung	lung
8	chr6:146866600-146883800	Weak transcription	Small Intestine	intestine
9	chr6:146866600-146885800	Weak transcription	Pancreas	Pancrea
10	chr6:146866800-146877600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:146866800-146878000	Weak transcription	Brain Substantia Nigra	brain
12	chr6:146867000-146876000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:146867000-146877200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:146867000-146877800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:146867000-146880600	Weak transcription	Right Ventricle	heart
16	chr6:146867200-146875600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:146867200-146875600	Weak transcription	Colonic Mucosa	Colon
18	chr6:146867200-146877800	Weak transcription	Primary T cells from cord blood	blood
19	chr6:146867400-146875400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:146867400-146875800	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:146867400-146877400	Weak transcription	Fetal Intestine Small	intestine
22	chr6:146867800-146875200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:146868000-146873800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:146868200-146876800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:146868400-146875200	Weak transcription	Right Atrium	heart
26	chr6:146868400-146875600	Weak transcription	HSMMtube	muscle
27	chr6:146868400-146876000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:146868600-146873400	Weak transcription	Stomach Mucosa	stomach
29	chr6:146868600-146875800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:146868800-146875600	Weak transcription	Hela-S3	cervix
31	chr6:146869600-146873800	Strong transcription	Osteobl	bone
32	chr6:146869600-146877000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:146870000-146873400	Genic enhancers	Monocytes-CD14+_RO01746	blood
34	chr6:146870000-146875800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:146870000-146876800	Strong transcription	HepG2	liver
36	chr6:146870000-146877000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:146870000-146877000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:146870200-146872800	Strong transcription	Liver	Liver
39	chr6:146870200-146873600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:146870200-146877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:146870400-146874000	Strong transcription	HUVEC	blood vessel
42	chr6:146870600-146872800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:146870600-146872800	Strong transcription	Thymus	Thymus
44	chr6:146870600-146873000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:146870600-146873000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:146870600-146873000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr6:146870600-146873000	Strong transcription	Ovary	ovary
48	chr6:146870600-146877000	Strong transcription	HSMM	muscle
49	chr6:146870800-146872800	Strong transcription	A549	lung
50	chr6:146870800-146873600	Strong transcription	Rectal Mucosa Donor 29	rectum

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