Variant report

Variant	rs45487791
Chromosome Location	chr2:54776993-54776994
allele	C/G
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	chr2:54776940-54777090	AG09309	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54770128..54773516-chr2:54775238..54777528,3	MCF-7	breast:
2	chr2:54763693..54765544-chr2:54775882..54778958,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234943	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11555856	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11904679	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12987967	0.83[EUR][1000 genomes]
rs13021615	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13036147	0.83[EUR][1000 genomes]
rs13391803	0.81[EUR][1000 genomes]
rs17039558	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17045939	0.83[EUR][1000 genomes]
rs34077590	0.83[EUR][1000 genomes]
rs34094680	0.86[EUR][1000 genomes]
rs34263579	0.88[EUR][1000 genomes]
rs34308676	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34429083	0.84[EUR][1000 genomes]
rs34978408	0.86[EUR][1000 genomes]
rs36018286	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796022	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4261758	0.87[EUR][1000 genomes]
rs4319969	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57281248	0.83[EUR][1000 genomes]
rs61126015	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66693131	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67079536	0.84[EUR][1000 genomes]
rs6734445	0.82[EUR][1000 genomes]
rs6734536	0.86[EUR][1000 genomes]
rs7586066	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs45487791	EML6	cis	Thyroid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
4	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:54769800-54777000	Weak transcription	Psoas Muscle	Psoas
6	chr2:54770000-54777400	Weak transcription	GM12878-XiMat	blood
7	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:54770600-54780200	Enhancers	Fetal Intestine Large	intestine
9	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:54772600-54778800	Enhancers	Brain Anterior Caudate	brain
11	chr2:54772600-54780200	Enhancers	Fetal Intestine Small	intestine
12	chr2:54773200-54777200	Weak transcription	NHLF	lung
13	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:54773800-54777000	Weak transcription	Aorta	Aorta
16	chr2:54773800-54782200	Weak transcription	Ovary	ovary
17	chr2:54774000-54777200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:54774000-54777400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:54774000-54779200	Enhancers	Duodenum Mucosa	Duodenum
20	chr2:54774000-54782400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:54774000-54782400	Weak transcription	Osteobl	bone
22	chr2:54774200-54778000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:54774200-54778000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:54774200-54779800	Weak transcription	NHDF-Ad	bronchial
25	chr2:54774400-54777000	Strong transcription	Fetal Lung	lung
26	chr2:54774600-54777000	Weak transcription	Fetal Kidney	kidney
27	chr2:54774600-54777800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:54774600-54778000	Enhancers	Fetal Brain Male	brain
29	chr2:54774800-54778400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:54774800-54778800	Enhancers	Brain Hippocampus Middle	brain
31	chr2:54774800-54781800	Weak transcription	Liver	Liver
32	chr2:54774800-54782400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:54775200-54778000	Enhancers	Fetal Brain Female	brain
34	chr2:54775400-54777000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:54775400-54777200	Genic enhancers	Fetal Muscle Leg	muscle
36	chr2:54775400-54777800	Enhancers	Gastric	stomach
37	chr2:54775400-54778600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr2:54775400-54778800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:54775400-54778800	Enhancers	Right Atrium	heart
40	chr2:54775400-54778800	Enhancers	Right Ventricle	heart
41	chr2:54775400-54778800	Enhancers	Small Intestine	intestine
42	chr2:54775400-54778800	Enhancers	Stomach Mucosa	stomach
43	chr2:54775400-54778800	Enhancers	HMEC	breast
44	chr2:54775400-54779000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:54775400-54779200	Genic enhancers	HepG2	liver
46	chr2:54775600-54777200	Strong transcription	Fetal Stomach	stomach
47	chr2:54775600-54779400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:54775800-54777000	Weak transcription	Lung	lung
49	chr2:54775800-54777600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:54775800-54778000	Weak transcription	Spleen	Spleen

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