Variant report

Variant	rs1149616
Chromosome Location	chr11:76498369-76498370
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	chr11:76498272-76500991	HepG2	liver:	n/a	n/a
2	SIN3AK20	chr11:76498338-76500863	MCF-7	breast:	n/a	n/a
3	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
4	BCL3	chr11:76498341-76500112	A549	lung:	n/a	chr11:76498984-76498993 chr11:76499454-76499461
5	ZKSCAN1	chr11:76498351-76498375	Hela-S3	cervix:	n/a	n/a
6	MXI1	chr11:76498161-76499904	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr11:76491706-76499377	A549	lung:	n/a	chr11:76495264-76495274 chr11:76499211-76499221 chr11:76492154-76492161 chr11:76499346-76499356 chr11:76492802-76492812
8	POLR2A	chr11:76497001-76500285	A549	lung:	n/a	n/a
9	POLR2A	chr11:76494484-76500840	A549	lung:	n/a	n/a
10	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	chr11:76493164..76499691-chr11:76510608..76517041,14	MCF-7	breast:
3	chr11:76482203..76483878-chr11:76496457..76499496,3	K562	blood:
4	chr11:76497872..76501557-chr11:76570027..76573455,3	K562	blood:
5	chr11:76497829..76500317-chr11:76518217..76520054,2	MCF-7	breast:
6	chr11:76496902..76499372-chr11:76570017..76571527,2	K562	blood:
7	chr11:76492689..76500449-chr11:76507700..76515545,17	K562	blood:
8	chr11:76484600..76489060-chr11:76497459..76500806,4	K562	blood:
9	chr11:76497234..76499501-chr11:76534793..76537709,2	K562	blood:
10	chr11:76450787..76452506-chr11:76497901..76500387,2	K562	blood:

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

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10899287	0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs11236934	0.87[YRI][hapmap]
rs1149597	0.89[CEU][hapmap]
rs1149599	0.83[CEU][hapmap]
rs1149605	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1149606	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs1149608	0.88[EUR][1000 genomes]
rs1149609	0.95[EUR][1000 genomes]
rs1149610	0.95[EUR][1000 genomes]
rs1149612	0.90[EUR][1000 genomes]
rs1149614	0.99[EUR][1000 genomes]
rs1149615	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1149617	0.97[EUR][1000 genomes]
rs1149618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1149619	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1149622	0.87[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs1224955	0.95[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs1664081	0.91[GIH][hapmap]
rs1687692	0.87[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs1687693	0.85[ASN][1000 genomes]
rs34909318	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35044108	0.82[ASN][1000 genomes]
rs3740776	0.86[EUR][1000 genomes]
rs3740777	0.95[EUR][1000 genomes]
rs881930	0.89[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1149616	RP11-21L23.3	cis	Adipose Subcutaneous	GTEx
rs1149616	POLD3	cis	parietal	SCAN
rs1149616	ACER3	cis	cerebellum	SCAN

Chromatin state (count:93 , 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	chr11:76496200-76498600	Enhancers	Brain Hippocampus Middle	brain
12	chr11:76496200-76499400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:76496200-76499800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr11:76496200-76503600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:76496200-76513800	Weak transcription	Fetal Kidney	kidney
16	chr11:76496400-76500600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:76496400-76500600	Enhancers	Fetal Heart	heart
18	chr11:76496400-76501000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:76496400-76501800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr11:76496400-76504000	Weak transcription	HSMMtube	muscle
21	chr11:76496600-76498400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr11:76496600-76498800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr11:76496600-76499200	Weak transcription	NH-A	brain
24	chr11:76496600-76500400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:76496600-76500800	Enhancers	Pancreas	Pancrea
26	chr11:76496600-76504400	Weak transcription	HUVEC	blood vessel
27	chr11:76496600-76509800	Weak transcription	Colon Smooth Muscle	Colon
28	chr11:76496800-76498400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr11:76496800-76498400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:76496800-76498600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:76496800-76498600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:76496800-76498600	Weak transcription	Fetal Intestine Large	intestine
33	chr11:76496800-76498600	Weak transcription	Gastric	stomach
34	chr11:76496800-76499000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr11:76496800-76499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:76496800-76499400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:76496800-76499400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr11:76496800-76499400	Genic enhancers	NHEK	skin
39	chr11:76496800-76500200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:76496800-76500200	Genic enhancers	Fetal Stomach	stomach
41	chr11:76496800-76500400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr11:76496800-76500800	Enhancers	Ovary	ovary
43	chr11:76496800-76501200	Enhancers	Duodenum Mucosa	Duodenum
44	chr11:76496800-76501400	Enhancers	Colonic Mucosa	Colon
45	chr11:76496800-76504200	Weak transcription	HSMM	muscle
46	chr11:76496800-76507400	Enhancers	Stomach Mucosa	stomach
47	chr11:76496800-76510000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:76497000-76498400	Enhancers	Right Atrium	heart
49	chr11:76497000-76498400	Genic enhancers	HMEC	breast
50	chr11:76497000-76498800	Weak transcription	Placenta Amnion	Placenta Amnion

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