Variant report

Variant	rs10890813
Chromosome Location	chr11:107987784-107987785
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:107987305-107987924	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:107979448-107987812	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:107984261..107988024-chr11:107989192..107992073,3	K562	blood:
2	chr11:107987486..107989883-chr11:107990743..107993337,2	K562	blood:

Variant related genes	Relation type
ACAT1	TF binding region
ENSG00000255467	Chromatin interaction
ENSG00000075239	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10890819	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10890820	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11212515	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12226047	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12226342	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs228593	1.00[ASW][hapmap];0.89[CEU][hapmap];0.80[TSI][hapmap]
rs228606	0.80[JPT][hapmap]
rs3741056	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4754297	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4987913	1.00[YRI][hapmap]
rs7114794	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928764	0.85[ASN][1000 genomes]
rs920679	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1039549	chr11:107950572-108034548	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10890813	ACAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs10890813	PDGFD	cis	cerebellum	SCAN
rs10890813	ACAT1	cis	cerebellum	SCAN
rs10890813	KDELC2	cis	Skin Sun Exposed Lower leg	GTEx
rs10890813	NPAT	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107953200-107991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr11:107955800-107991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:107966400-107992000	Weak transcription	Fetal Brain Male	brain
4	chr11:107967000-107991400	Weak transcription	A549	lung
5	chr11:107968200-107992000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:107969000-107991600	Weak transcription	Hela-S3	cervix
7	chr11:107969200-107991800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:107970600-107991600	Weak transcription	HepG2	liver
9	chr11:107972400-107991400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr11:107972400-107991600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:107972400-107992000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:107972600-107992200	Weak transcription	Gastric	stomach
13	chr11:107973400-107991800	Weak transcription	Primary T cells from cord blood	blood
14	chr11:107973600-107991600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:107973600-107991800	Weak transcription	Primary B cells from cord blood	blood
16	chr11:107973600-107991800	Weak transcription	Brain Germinal Matrix	brain
17	chr11:107973600-107991800	Weak transcription	Fetal Brain Female	brain
18	chr11:107973800-107991600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr11:107973800-107991800	Weak transcription	Lung	lung
20	chr11:107973800-107992000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:107974200-107991800	Weak transcription	Thymus	Thymus
22	chr11:107974600-107991800	Weak transcription	HUVEC	blood vessel
23	chr11:107974800-107992000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:107975400-107991600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:107975400-107991800	Weak transcription	Fetal Intestine Large	intestine
26	chr11:107975400-107991800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr11:107975400-107991800	Weak transcription	GM12878-XiMat	blood
28	chr11:107975600-107991400	Weak transcription	Dnd41	blood
29	chr11:107975800-107991600	Weak transcription	Placenta	Placenta
30	chr11:107975800-107991800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr11:107976600-107991800	Weak transcription	Fetal Thymus	thymus
32	chr11:107977000-107991400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:107977000-107991800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr11:107977200-107991600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:107977200-107991600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr11:107977200-107991800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:107977800-107991800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr11:107978200-107991800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr11:107980200-107991800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:107981600-107991800	Weak transcription	Fetal Intestine Small	intestine
41	chr11:107982400-107991800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:107985600-107987800	Enhancers	Rectal Smooth Muscle	rectum
43	chr11:107986600-107992000	Weak transcription	Pancreas	Pancrea
44	chr11:107986800-107991200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:107986800-107991800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:107986800-107991800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr11:107986800-107991800	Weak transcription	Stomach Mucosa	stomach
48	chr11:107986800-107992000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr11:107987000-107991400	Weak transcription	Adipose Nuclei	Adipose
50	chr11:107987000-107991600	Weak transcription	Brain Inferior Temporal Lobe	brain

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