Variant report

Variant	rs920679
Chromosome Location	chr11:108038477-108038478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10890813	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs10890819	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10890820	0.81[EUR][1000 genomes]
rs10890825	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11212515	0.94[CEU][hapmap];0.85[JPT][hapmap]
rs170548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs227060	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs228593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs228606	0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs373759	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs3741056	0.89[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs61913701	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs665293	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7114794	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs7129527	0.84[ASN][1000 genomes]
rs7928764	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1040522	chr11:107969357-108049672	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs920679	NPAT	cis	cerebellum	SCAN
rs920679	ACAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs920679	ACAT1	cis	cerebellum	SCAN
rs920679	PDGFD	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107993200-108069600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:108002200-108069600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr11:108002400-108040200	Strong transcription	Liver	Liver
4	chr11:108002800-108048000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr11:108003600-108040800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:108005800-108040800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr11:108009000-108041000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:108009200-108071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:108009400-108040400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:108009400-108062600	Strong transcription	Primary T cells from cord blood	blood
11	chr11:108009400-108068400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:108009600-108041800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr11:108009600-108049000	Strong transcription	Placenta	Placenta
14	chr11:108009600-108068200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:108009800-108048000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr11:108010600-108071200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:108010800-108038800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:108010800-108041400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:108010800-108041800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:108010800-108049200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:108011600-108044200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr11:108011800-108047800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:108015600-108045000	Weak transcription	Stomach Mucosa	stomach
24	chr11:108016200-108039800	Weak transcription	Fetal Heart	heart
25	chr11:108017000-108075000	Strong transcription	Dnd41	blood
26	chr11:108018200-108040600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:108019000-108040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:108019000-108043800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:108021000-108039400	Weak transcription	Brain Angular Gyrus	brain
30	chr11:108022800-108043000	Weak transcription	Colonic Mucosa	Colon
31	chr11:108022800-108052600	Weak transcription	Spleen	Spleen
32	chr11:108023000-108053000	Weak transcription	Pancreas	Pancrea
33	chr11:108023000-108055400	Weak transcription	Esophagus	oesophagus
34	chr11:108023800-108041000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:108023800-108053200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:108024600-108047600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:108024800-108070400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:108025600-108041600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:108025800-108041000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:108026200-108072200	Strong transcription	Fetal Thymus	thymus
41	chr11:108026600-108040800	Weak transcription	NHLF	lung
42	chr11:108026600-108047200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr11:108026800-108071000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr11:108027000-108069800	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr11:108028000-108041000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr11:108028800-108041800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr11:108028800-108068000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr11:108029200-108067800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:108029400-108041800	Strong transcription	Brain Germinal Matrix	brain
50	chr11:108029600-108040800	Strong transcription	Fetal Muscle Trunk	muscle

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