Variant report

Variant	rs12801988
Chromosome Location	chr11:108357747-108357748
allele	C/T
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	TEAD4	chr11:108357609-108357886	K562	blood:	n/a	n/a
2	EP300	chr11:108357705-108357873	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:108357626..108360245-chr11:108366934..108369201,3	MCF-7	breast:
2	chr11:108338406..108340928-chr11:108356755..108359282,2	K562	blood:
3	chr11:108357100..108360869-chr11:108361968..108364504,3	K562	blood:

Variant related genes	Relation type
KDELC2	TF binding region
ENSG00000221607	Chromatin interaction
ENSG00000178202	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10431060	0.82[EUR][1000 genomes]
rs10749917	0.81[ASN][1000 genomes]
rs10749918	0.89[ASN][1000 genomes]
rs10789659	0.84[EUR][1000 genomes]
rs10789665	0.90[ASN][1000 genomes]
rs10890848	0.81[ASN][1000 genomes]
rs10890849	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11212610	0.83[EUR][1000 genomes]
rs11212619	0.84[EUR][1000 genomes]
rs11212635	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11212640	0.90[EUR][1000 genomes]
rs11212659	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11212661	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11212666	0.80[ASN][1000 genomes]
rs11212676	0.81[ASN][1000 genomes]
rs113995	0.81[EUR][1000 genomes]
rs12223381	0.88[ASN][1000 genomes]
rs12419828	0.82[ASN][1000 genomes]
rs12792979	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12796446	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1583598	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs172895	0.81[EUR][1000 genomes]
rs186594	0.81[EUR][1000 genomes]
rs186595	0.81[EUR][1000 genomes]
rs2118309	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs227054	0.84[EUR][1000 genomes]
rs227064	0.80[EUR][1000 genomes]
rs227066	0.81[EUR][1000 genomes]
rs227070	0.80[EUR][1000 genomes]
rs227075	0.80[EUR][1000 genomes]
rs227077	0.81[EUR][1000 genomes]
rs227086	0.82[EUR][1000 genomes]
rs227087	0.82[EUR][1000 genomes]
rs227088	0.82[EUR][1000 genomes]
rs227091	0.81[EUR][1000 genomes]
rs227092	0.82[EUR][1000 genomes]
rs227093	0.82[EUR][1000 genomes]
rs227094	0.82[EUR][1000 genomes]
rs374443	0.80[EUR][1000 genomes]
rs3765632	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3824987	0.81[ASN][1000 genomes]
rs3901851	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs425538	0.80[EUR][1000 genomes]
rs4585	0.82[EUR][1000 genomes]
rs4754318	0.82[EUR][1000 genomes]
rs4754324	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5023001	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs573890	0.81[EUR][1000 genomes]
rs605394	0.85[EUR][1000 genomes]
rs60683001	0.81[EUR][1000 genomes]
rs609655	0.80[EUR][1000 genomes]
rs61913892	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61915104	0.81[EUR][1000 genomes]
rs652311	0.82[EUR][1000 genomes]
rs652541	0.80[EUR][1000 genomes]
rs664143	0.80[EUR][1000 genomes]
rs7112136	0.84[EUR][1000 genomes]
rs7120845	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7126588	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751343	0.91[ASN][1000 genomes]
rs7931930	0.82[EUR][1000 genomes]
rs7934719	0.87[ASN][1000 genomes]
rs7942014	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7943203	0.85[ASN][1000 genomes]
rs7943607	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs893279	0.80[ASN][1000 genomes]
rs9667658	0.83[AMR][1000 genomes];0.86[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	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
3	nsv832263	chr11:108183372-108384391	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12801988	ACAT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108338200-108359000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:108338200-108367600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:108338600-108364800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr11:108338600-108367200	Weak transcription	A549	lung
5	chr11:108338600-108367800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:108338800-108367200	Weak transcription	HSMMtube	muscle
7	chr11:108338800-108367400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:108338800-108367400	Weak transcription	HUVEC	blood vessel
9	chr11:108338800-108367600	Weak transcription	Brain Angular Gyrus	brain
10	chr11:108338800-108367600	Weak transcription	Small Intestine	intestine
11	chr11:108338800-108368000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:108339000-108359000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:108339000-108367200	Weak transcription	NHEK	skin
14	chr11:108339000-108367400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:108339000-108368000	Weak transcription	Primary B cells from cord blood	blood
16	chr11:108339000-108368000	Weak transcription	Fetal Brain Female	brain
17	chr11:108339200-108363000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:108339200-108367400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:108339200-108367600	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:108339200-108367800	Weak transcription	Fetal Brain Male	brain
21	chr11:108339200-108368000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:108343000-108361800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:108344000-108361800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:108344000-108362000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:108344000-108363000	Strong transcription	Dnd41	blood
26	chr11:108344200-108361800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:108344200-108362000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:108344600-108361000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr11:108345000-108358200	Strong transcription	Primary T cells from cord blood	blood
30	chr11:108345800-108359000	Weak transcription	Gastric	stomach
31	chr11:108346000-108364800	Weak transcription	Fetal Heart	heart
32	chr11:108346000-108367200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr11:108346000-108367600	Weak transcription	Brain Substantia Nigra	brain
34	chr11:108347200-108358200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:108347400-108361800	Strong transcription	Liver	Liver
36	chr11:108348400-108364800	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:108348400-108367400	Weak transcription	Colonic Mucosa	Colon
38	chr11:108348400-108367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:108348600-108367200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:108348600-108367200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr11:108348600-108367400	Weak transcription	Esophagus	oesophagus
42	chr11:108348600-108367600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:108348800-108367600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr11:108349200-108358000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:108349200-108367200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:108350000-108367400	Weak transcription	Hela-S3	cervix
47	chr11:108350200-108359200	Weak transcription	NHDF-Ad	bronchial
48	chr11:108350200-108367400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr11:108350200-108367400	Weak transcription	Fetal Kidney	kidney
50	chr11:108350400-108367400	Weak transcription	Brain Anterior Caudate	brain

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