Variant report

Variant	rs10789666
Chromosome Location	chr11:108397460-108397461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:108391880..108394458-chr11:108395000..108399598,4	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10749920	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890853	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10890855	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890858	0.84[CEU][hapmap]
rs10890859	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11212682	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11212689	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11212691	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11212695	0.80[EUR][1000 genomes]
rs11212700	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11212704	0.92[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs11824250	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12362341	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17092330	0.82[CEU][hapmap]
rs1940219	0.84[CEU][hapmap]
rs2016291	0.90[EUR][1000 genomes]
rs2846412	0.95[LWK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs3741060	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs3900699	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4442514	0.84[CEU][hapmap]
rs4533001	0.84[CEU][hapmap]
rs4643041	0.97[EUR][1000 genomes]
rs4753844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754326	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7104503	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7118229	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10789666	ACAT1	cis	cerebellum	SCAN
rs10789666	KDELC2	Cis_1M	lymphoblastoid	RTeQTL
rs10789666	KDELC2	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108370400-108408800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:108371800-108406400	Weak transcription	Gastric	stomach
3	chr11:108372000-108401200	Weak transcription	Esophagus	oesophagus
4	chr11:108381000-108408800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr11:108383000-108398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:108385000-108409000	Weak transcription	Fetal Kidney	kidney
7	chr11:108385000-108414000	Weak transcription	HSMM	muscle
8	chr11:108385000-108422800	Weak transcription	Fetal Intestine Small	intestine
9	chr11:108385200-108403600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:108385400-108409200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:108385600-108402600	Weak transcription	Brain Anterior Caudate	brain
12	chr11:108385600-108405000	Weak transcription	HMEC	breast
13	chr11:108385600-108405200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:108385600-108408400	Weak transcription	Aorta	Aorta
15	chr11:108385600-108408800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:108385600-108409400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:108385600-108412400	Weak transcription	HSMMtube	muscle
18	chr11:108392000-108397800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr11:108395000-108398800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:108395400-108398600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:108395800-108398600	Strong transcription	NHEK	skin
22	chr11:108396200-108401200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:108396200-108401400	Weak transcription	Lung	lung
24	chr11:108396200-108408800	Strong transcription	Placenta	Placenta
25	chr11:108396200-108408800	Weak transcription	Pancreas	Pancrea
26	chr11:108396400-108409000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:108397000-108397800	Strong transcription	K562	blood
28	chr11:108397000-108399000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr11:108397000-108399200	Strong transcription	Liver	Liver
30	chr11:108397000-108400000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:108397200-108398800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:108397400-108405000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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