Variant report

Variant	rs354241
Chromosome Location	chr2:54951888-54951889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs241662	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2567837	0.92[EUR][1000 genomes]
rs354188	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs354215	0.80[EUR][1000 genomes]
rs354239	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs354242	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][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	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
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3362527	chr2:54951248-54953146	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs354241	EML6	cis	Artery Tibial	GTEx
rs354241	EML6	cis	Esophagus Muscularis	GTEx
rs354241	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54949800-54952600	Active TSS	Psoas Muscle	Psoas
2	chr2:54949800-54952800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr2:54950000-54952000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:54950000-54952000	Active TSS	Sigmoid Colon	Sigmoid Colon
5	chr2:54950000-54952200	Active TSS	Esophagus	oesophagus
6	chr2:54950000-54952200	Active TSS	Gastric	stomach
7	chr2:54950000-54952200	Active TSS	Left Ventricle	heart
8	chr2:54950000-54952200	Active TSS	Lung	lung
9	chr2:54950000-54952400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:54950000-54952400	Active TSS	Aorta	Aorta
11	chr2:54950000-54952600	Active TSS	Right Atrium	heart
12	chr2:54950000-54952600	Active TSS	Right Ventricle	heart
13	chr2:54950000-54953400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr2:54950200-54952000	Active TSS	Small Intestine	intestine
15	chr2:54950200-54952200	Active TSS	Pancreas	Pancrea
16	chr2:54950200-54952200	Active TSS	Spleen	Spleen
17	chr2:54950200-54952400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:54950200-54952400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr2:54950200-54952400	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr2:54950200-54952400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:54950200-54952400	Active TSS	Brain Anterior Caudate	brain
22	chr2:54950200-54952400	Active TSS	Ovary	ovary
23	chr2:54950200-54952400	Active TSS	NHDF-Ad	bronchial
24	chr2:54950200-54952600	Active TSS	Brain Hippocampus Middle	brain
25	chr2:54950200-54952600	Active TSS	Brain Substantia Nigra	brain
26	chr2:54950200-54952600	Active TSS	NHLF	lung
27	chr2:54950200-54953200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr2:54950200-54953400	Active TSS	Brain Cingulate Gyrus	brain
29	chr2:54950200-54953600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:54950200-54954400	Active TSS	Brain Angular Gyrus	brain
31	chr2:54950400-54954000	Active TSS	Fetal Brain Female	brain
32	chr2:54950600-54952200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:54950800-54952800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
34	chr2:54950800-54953000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr2:54951000-54952000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
36	chr2:54951000-54952000	Flanking Active TSS	HMEC	breast
37	chr2:54951000-54952200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:54951000-54952200	Flanking Active TSS	Liver	Liver
39	chr2:54951000-54952200	Flanking Active TSS	HUVEC	blood vessel
40	chr2:54951000-54952400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:54951000-54952400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr2:54951000-54952600	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:54951000-54952800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
44	chr2:54951000-54952800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:54951000-54953000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr2:54951200-54952000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr2:54951200-54952000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:54951200-54952000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
49	chr2:54951200-54952000	Flanking Bivalent TSS/Enh	NH-A	brain
50	chr2:54951200-54952400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell

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