Variant report

Variant	rs1149612
Chromosome Location	chr11:76496736-76496737
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	CTCF	chr11:76496640-76496790	HepG2	liver:	n/a	n/a
2	BCL3	chr11:76495697-76498146	A549	lung:	n/a	chr11:76497573-76497581
3	ZNF263	chr11:76496431-76496842	HEK293-T-REx	kidney:	n/a	n/a
4	POLR2A	chr11:76491728-76497876	HepG2	liver:	n/a	n/a
5	CTCF	chr11:76496640-76496790	AoAF	blood vessel:	n/a	n/a
6	POLR2A	chr11:76496497-76496806	Hela-S3	cervix:	n/a	n/a
7	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
8	CTCF	chr11:76496720-76496870	NHDF-neo	bronchial:	n/a	n/a
9	POLR2A	chr11:76496288-76496902	A549	lung:	n/a	n/a
10	RCOR1	chr11:76493287-76496988	IMR90	lung:	n/a	n/a
11	POLR2A	chr11:76493270-76497083	IMR90	lung:	n/a	n/a
12	POLR2A	chr11:76496433-76496811	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr11:76496507-76496808	A549	lung:	n/a	n/a
14	SIN3AK20	chr11:76496487-76497084	A549	lung:	n/a	n/a
15	POLR2A	chr11:76496301-76496931	A549	lung:	n/a	n/a
16	SIN3A	chr11:76496670-76496870	H1-hESC	embryonic stem cell:	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	FOSL2	chr11:76495934-76497552	A549	lung:	n/a	n/a
19	POLR2A	chr11:76496272-76496896	A549	lung:	n/a	n/a
20	POLR2A	chr11:76494484-76500840	A549	lung:	n/a	n/a
21	REST	chr11:76494996-76496840	A549	lung:	n/a	chr11:76495279-76495297 chr11:76495766-76495779 chr11:76495087-76495100

No.	Distal block	Cell Line	Cell type
1	chr11:76444941..76446826-chr11:76495647..76497317,2	K562	blood:
2	chr11:76493164..76499691-chr11:76510608..76517041,14	MCF-7	breast:
3	chr11:76449564..76451543-chr11:76496131..76497754,2	MCF-7	breast:
4	chr11:76482203..76483878-chr11:76496457..76499496,3	K562	blood:
5	chr11:76495179..76497030-chr13:37572998..37574971,2	MCF-7	breast:
6	chr11:76492689..76500449-chr11:76507700..76515545,17	K562	blood:

Variant related genes	Relation type
ENSG00000255100	TF binding region
ENSG00000120697	Chromatin interaction
ENSG00000120699	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];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149608	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149609	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1149610	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1149614	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1149615	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1149616	0.90[EUR][1000 genomes]
rs1149617	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1149618	0.87[EUR][1000 genomes]
rs1149619	0.86[EUR][1000 genomes]
rs1224955	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1664081	0.84[ASN][1000 genomes]
rs34909318	0.89[EUR][1000 genomes]
rs3740776	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3740777	0.89[AMR][1000 genomes];0.89[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
rs1149612	RP11-21L23.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76494000-76496800	Active TSS	Gastric	stomach
2	chr11:76495000-76498000	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr11:76495400-76501800	Transcr. at gene 5' and 3'	A549	lung
4	chr11:76495600-76496800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:76495600-76496800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:76495600-76496800	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr11:76495600-76496800	Active TSS	Right Atrium	heart
8	chr11:76495600-76497800	Flanking Active TSS	Fetal Brain Female	brain
9	chr11:76495600-76497800	Enhancers	Spleen	Spleen
10	chr11:76495800-76496800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:76495800-76496800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr11:76495800-76496800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:76495800-76496800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:76495800-76496800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:76495800-76496800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:76495800-76496800	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr11:76495800-76496800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr11:76495800-76496800	Flanking Active TSS	HMEC	breast
19	chr11:76495800-76498000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr11:76495800-76499600	Weak transcription	Brain Substantia Nigra	brain
21	chr11:76496000-76496800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:76496000-76496800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:76496000-76496800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr11:76496000-76496800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr11:76496000-76496800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:76496000-76496800	Flanking Active TSS	Ovary	ovary
27	chr11:76496000-76496800	Flanking Active TSS	Stomach Mucosa	stomach
28	chr11:76496000-76496800	Active TSS	Stomach Smooth Muscle	stomach
29	chr11:76496000-76496800	Flanking Active TSS	HepG2	liver
30	chr11:76496000-76496800	Transcr. at gene 5' and 3'	NHEK	skin
31	chr11:76496000-76497000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr11:76496000-76497200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr11:76496000-76497200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:76496000-76497200	Weak transcription	Left Ventricle	heart
35	chr11:76496000-76497400	Bivalent Enhancer	Fetal Thymus	thymus
36	chr11:76496000-76497800	Flanking Active TSS	Liver	Liver
37	chr11:76496000-76497800	Enhancers	Fetal Lung	lung
38	chr11:76496000-76497800	Transcr. at gene 5' and 3'	Hela-S3	cervix
39	chr11:76496000-76499000	Weak transcription	Lung	lung
40	chr11:76496000-76499200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr11:76496000-76499400	Weak transcription	Brain Anterior Caudate	brain
42	chr11:76496000-76499600	Weak transcription	Brain Angular Gyrus	brain
43	chr11:76496000-76499800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:76496000-76500600	Enhancers	Fetal Muscle Trunk	muscle
45	chr11:76496000-76501000	Enhancers	Right Ventricle	heart
46	chr11:76496000-76506800	Weak transcription	Aorta	Aorta
47	chr11:76496200-76496800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
48	chr11:76496200-76496800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:76496200-76496800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:76496200-76496800	Flanking Active TSS	Esophagus	oesophagus

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