Variant report

Variant	rs11749113
Chromosome Location	chr5:80530531-80530532
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	chr5:80530046..80533018-chr5:80537820..80540645,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248794	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10514218	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs10942946	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11739834	0.93[AFR][1000 genomes]
rs11743842	0.83[AFR][1000 genomes]
rs11743849	0.93[AFR][1000 genomes]
rs11745275	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11953113	0.83[EUR][1000 genomes]
rs11957137	0.83[EUR][1000 genomes]
rs12516089	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12517538	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12518716	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12523578	1.00[CEU][hapmap]
rs16878594	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16878597	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62364993	0.80[EUR][1000 genomes]
rs62365025	0.92[EUR][1000 genomes]
rs62365032	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62365035	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62365038	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72771170	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7731320	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11749113	CTC-281B15.1	cis	lung	GTEx
rs11749113	CTC-281B15.1	cis	Artery Aorta	GTEx
rs11749113	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs11749113	CTC-281B15.1	cis	Thyroid	GTEx
rs11749113	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs11749113	CTC-281B15.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11749113	CTC-281B15.1	cis	Artery Tibial	GTEx
rs11749113	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs11749113	CTC-281B15.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80525800-80531000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:80526600-80531200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
5	chr5:80528200-80531000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:80528200-80531800	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr5:80528400-80531600	Enhancers	Spleen	Spleen
8	chr5:80528600-80531400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr5:80528600-80531600	Enhancers	Fetal Thymus	thymus
10	chr5:80528600-80532000	Enhancers	Lung	lung
11	chr5:80528800-80531000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:80528800-80531400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:80528800-80531400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr5:80529000-80530800	Active TSS	Left Ventricle	heart
15	chr5:80529400-80530600	Weak transcription	Esophagus	oesophagus
16	chr5:80529400-80531400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:80529400-80531600	Weak transcription	Gastric	stomach
18	chr5:80529400-80531800	Weak transcription	Fetal Brain Female	brain
19	chr5:80529400-80532400	Weak transcription	Placenta	Placenta
20	chr5:80529400-80532400	Active TSS	Right Ventricle	heart
21	chr5:80529400-80535200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:80529400-80540800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:80529400-80541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:80529400-80543400	Weak transcription	NHLF	lung
25	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:80529600-80530600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:80529600-80530600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr5:80529600-80530800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr5:80529600-80530800	Weak transcription	Fetal Intestine Small	intestine
31	chr5:80529600-80531000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:80529600-80531000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:80529600-80531000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:80529600-80531200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr5:80529600-80531200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr5:80529600-80531200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr5:80529600-80531200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:80529600-80531200	Weak transcription	Fetal Lung	lung
39	chr5:80529600-80531200	Enhancers	HepG2	liver
40	chr5:80529600-80531200	Weak transcription	K562	blood
41	chr5:80529600-80531400	Weak transcription	Stomach Mucosa	stomach
42	chr5:80529600-80532000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr5:80529600-80532200	Enhancers	Adipose Nuclei	Adipose
44	chr5:80529600-80532400	Enhancers	Brain Anterior Caudate	brain
45	chr5:80529600-80535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:80529600-80541000	Weak transcription	Fetal Intestine Large	intestine
47	chr5:80529600-80542800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:80529800-80530600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:80529800-80530600	Enhancers	HUES48 Cell Line	embryonic stem cell

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