Variant report

Variant	rs1149617
Chromosome Location	chr11:76498780-76498781
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	POLR2A	chr11:76498642-76499448	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:76498272-76500991	HepG2	liver:	n/a	n/a
3	MAX	chr11:76498722-76500332	HCT-116	colon:	n/a	chr11:76499004-76499014 chr11:76500087-76500096
4	POLR2A	chr11:76498722-76499004	Hela-S3	cervix:	n/a	n/a
5	MYC	chr11:76498735-76500092	MCF10A-Er-Src	breast:	n/a	chr11:76499004-76499014
6	SIN3AK20	chr11:76498338-76500863	MCF-7	breast:	n/a	n/a
7	POLR2A	chr11:76498512-76498882	A549	lung:	n/a	n/a
8	EP300	chr11:76498679-76499179	HepG2	liver:	n/a	chr11:76498979-76498993
9	MAX	chr11:76491870-76500240	A549	lung:	n/a	chr11:76495789-76495799 chr11:76494160-76494170 chr11:76494949-76494959 chr11:76499004-76499014 chr11:76494703-76494719 chr11:76500087-76500096
10	SP1	chr11:76498654-76499204	A549	lung:	n/a	n/a
11	CEBPB	chr11:76498741-76500149	MCF-7	breast:	n/a	chr11:76499051-76499068
12	BCL3	chr11:76498341-76500112	A549	lung:	n/a	chr11:76498984-76498993 chr11:76499454-76499461
13	MXI1	chr11:76498522-76499231	IMR90	lung:	n/a	n/a
14	MAX	chr11:76498548-76499738	K562	blood:	n/a	chr11:76499004-76499014
15	MAX	chr11:76498395-76500693	MCF-7	breast:	n/a	chr11:76499004-76499014 chr11:76500087-76500096
16	MXI1	chr11:76498161-76499904	SK-N-SH	brain:	n/a	n/a
17	TCF12	chr11:76491706-76499377	A549	lung:	n/a	chr11:76495264-76495274 chr11:76499211-76499221 chr11:76492154-76492161 chr11:76499346-76499356 chr11:76492802-76492812
18	POLR2A	chr11:76497001-76500285	A549	lung:	n/a	n/a
19	POLR2A	chr11:76498581-76498792	A549	lung:	n/a	n/a
20	POLR2A	chr11:76494484-76500840	A549	lung:	n/a	n/a
21	POLR2A	chr11:76498620-76499179	HepG2	liver:	n/a	n/a
22	BCL3	chr11:76498367-76499278	A549	lung:	n/a	chr11:76498984-76498993

No.	Distal block	Cell Line	Cell type
1	chr11:76497529..76499535-chr11:76534642..76536244,2	MCF-7	breast:
2	chr11:76464979..76468586-chr11:76498537..76501368,3	MCF-7	breast:
3	chr11:76475834..76477640-chr11:76498585..76500944,2	K562	blood:
4	chr11:76493164..76499691-chr11:76510608..76517041,14	MCF-7	breast:
5	chr11:76482203..76483878-chr11:76496457..76499496,3	K562	blood:
6	chr11:76498398..76500983-chr11:76629016..76630524,2	MCF-7	breast:
7	chr11:76497872..76501557-chr11:76570027..76573455,3	K562	blood:
8	chr11:76497829..76500317-chr11:76518217..76520054,2	MCF-7	breast:
9	chr11:76496902..76499372-chr11:76570017..76571527,2	K562	blood:
10	chr11:76492689..76500449-chr11:76507700..76515545,17	K562	blood:
11	chr11:76484600..76489060-chr11:76497459..76500806,4	K562	blood:
12	chr11:76497234..76499501-chr11:76534793..76537709,2	K562	blood:
13	chr11:76450787..76452506-chr11:76497901..76500387,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACER3-1	chr11:76498677-76500442	NONHSAT023191

Variant related genes	Relation type
TSKU	TF binding region
ENSG00000255100	TF binding region
ENSG00000078124	Chromatin interaction
ENSG00000261578	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1149606	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1149608	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149609	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1149610	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1149612	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1149614	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1149615	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1149616	0.97[EUR][1000 genomes]
rs1149618	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1149619	0.97[EUR][1000 genomes]
rs1224955	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1664081	0.85[ASN][1000 genomes]
rs34909318	0.94[EUR][1000 genomes]
rs3740776	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3740777	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897931	chr11:76489673-76540708	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1149617	RP11-21L23.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76495400-76501800	Transcr. at gene 5' and 3'	A549	lung
2	chr11:76495800-76499600	Weak transcription	Brain Substantia Nigra	brain
3	chr11:76496000-76499000	Weak transcription	Lung	lung
4	chr11:76496000-76499200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:76496000-76499400	Weak transcription	Brain Anterior Caudate	brain
6	chr11:76496000-76499600	Weak transcription	Brain Angular Gyrus	brain
7	chr11:76496000-76499800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:76496000-76500600	Enhancers	Fetal Muscle Trunk	muscle
9	chr11:76496000-76501000	Enhancers	Right Ventricle	heart
10	chr11:76496000-76506800	Weak transcription	Aorta	Aorta
11	chr11:76496200-76499400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:76496200-76499800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr11:76496200-76503600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:76496200-76513800	Weak transcription	Fetal Kidney	kidney
15	chr11:76496400-76500600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:76496400-76500600	Enhancers	Fetal Heart	heart
17	chr11:76496400-76501000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:76496400-76501800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:76496400-76504000	Weak transcription	HSMMtube	muscle
20	chr11:76496600-76498800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr11:76496600-76499200	Weak transcription	NH-A	brain
22	chr11:76496600-76500400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:76496600-76500800	Enhancers	Pancreas	Pancrea
24	chr11:76496600-76504400	Weak transcription	HUVEC	blood vessel
25	chr11:76496600-76509800	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:76496800-76499000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr11:76496800-76499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:76496800-76499400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:76496800-76499400	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr11:76496800-76499400	Genic enhancers	NHEK	skin
31	chr11:76496800-76500200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:76496800-76500200	Genic enhancers	Fetal Stomach	stomach
33	chr11:76496800-76500400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr11:76496800-76500800	Enhancers	Ovary	ovary
35	chr11:76496800-76501200	Enhancers	Duodenum Mucosa	Duodenum
36	chr11:76496800-76501400	Enhancers	Colonic Mucosa	Colon
37	chr11:76496800-76504200	Weak transcription	HSMM	muscle
38	chr11:76496800-76507400	Enhancers	Stomach Mucosa	stomach
39	chr11:76496800-76510000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:76497000-76498800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr11:76497200-76499600	Weak transcription	Small Intestine	intestine
42	chr11:76497200-76500000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr11:76497200-76500600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:76497200-76500800	Enhancers	Left Ventricle	heart
45	chr11:76497400-76498800	Enhancers	HepG2	liver
46	chr11:76497400-76499400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:76497400-76501200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr11:76497400-76502200	Weak transcription	Brain Germinal Matrix	brain
49	chr11:76497600-76498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr11:76497800-76499000	Genic enhancers	Hela-S3	cervix

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