Variant report

Variant	rs354242
Chromosome Location	chr2:54951453-54951454
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	RFX5	chr2:54949181-54951799	IMR90	lung:	n/a	chr2:54950701-54950716
2	ZNF263	chr2:54950020-54951506	HEK293-T-REx	kidney:	n/a	n/a
3	KAP1	chr2:54949980-54951649	HEK293	kidney:	n/a	chr2:54951554-54951562
4	SMARCC1	chr2:54949807-54951484	Hela-S3	cervix:	n/a	chr2:54950598-54950607
5	SRF	chr2:54951386-54951563	HepG2	liver:	n/a	n/a
6	MTA3	chr2:54949926-54951464	GM12878	blood:	n/a	n/a
7	MAX	chr2:54950144-54951461	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr2:54949717-54952029	Raji	blood:	n/a	n/a
9	MYC	chr2:54951143-54951472	MCF10A-Er-Src	breast:	n/a	n/a
10	MAX	chr2:54950029-54951996	A549	lung:	n/a	n/a
11	MXI1	chr2:54949356-54954156	SK-N-SH	brain:	n/a	chr2:54949674-54949689
12	MYBL2	chr2:54949779-54951665	HepG2	liver:	n/a	n/a
13	HA-E2F1	chr2:54949666-54952092	MCF-7	breast:	n/a	chr2:54952002-54952012 chr2:54949703-54949712 chr2:54952005-54952015 chr2:54952022-54952032 chr2:54950557-54950572
14	TCF12	chr2:54949953-54951587	A549	lung:	n/a	n/a
15	E2F6	chr2:54950106-54951885	A549	lung:	n/a	chr2:54950402-54950413 chr2:54950557-54950572
16	RFX5	chr2:54949786-54952096	SK-N-SH	brain:	n/a	chr2:54950701-54950716
17	MAX	chr2:54950045-54951483	NB4	blood:	n/a	n/a
18	POLR2A	chr2:54950215-54951493	H1-neurons	neurons:	n/a	n/a
19	REST	chr2:54950280-54951570	H1-neurons	neurons:	n/a	chr2:54950402-54950412
20	SIN3A	chr2:54950023-54952434	H1-hESC	embryonic stem cell:	n/a	chr2:54950992-54951003
21	SMC3	chr2:54949772-54951580	Hela-S3	cervix:	n/a	chr2:54950012-54950019
22	HDAC2	chr2:54949985-54951479	HepG2	liver:	n/a	n/a
23	HCFC1	chr2:54949547-54951672	Hela-S3	cervix:	n/a	n/a
24	MAX	chr2:54949795-54952040	A549	lung:	n/a	n/a
25	JUN	chr2:54951417-54951550	H1-hESC	embryonic stem cell:	n/a	n/a
26	MXI1	chr2:54949594-54952119	IMR90	lung:	n/a	chr2:54949674-54949689
27	POLR2A	chr2:54950233-54952385	H1-neurons	neurons:	n/a	n/a
28	JUND	chr2:54950386-54951460	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
EML6	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1848923	0.90[ASN][1000 genomes]
rs241662	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2567837	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666036	0.83[AFR][1000 genomes]
rs354188	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs354191	0.85[AFR][1000 genomes]
rs354193	0.96[AFR][1000 genomes]
rs354215	0.81[EUR][1000 genomes]
rs354239	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs354241	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671229	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs72618666	0.89[ASN][1000 genomes]
rs72618669	0.90[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs354242	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL
rs354242	EML6	cis	Artery Tibial	GTEx
rs354242	EML6	cis	Artery Aorta	GTEx
rs354242	EML6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54949800-54951600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:54949800-54951800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:54949800-54952600	Active TSS	Psoas Muscle	Psoas
4	chr2:54949800-54952800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:54950000-54952000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:54950000-54952000	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr2:54950000-54952200	Active TSS	Esophagus	oesophagus
8	chr2:54950000-54952200	Active TSS	Gastric	stomach
9	chr2:54950000-54952200	Active TSS	Left Ventricle	heart
10	chr2:54950000-54952200	Active TSS	Lung	lung
11	chr2:54950000-54952400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:54950000-54952400	Active TSS	Aorta	Aorta
13	chr2:54950000-54952600	Active TSS	Right Atrium	heart
14	chr2:54950000-54952600	Active TSS	Right Ventricle	heart
15	chr2:54950000-54953400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:54950200-54951600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:54950200-54952000	Active TSS	Small Intestine	intestine
18	chr2:54950200-54952200	Active TSS	Pancreas	Pancrea
19	chr2:54950200-54952200	Active TSS	Spleen	Spleen
20	chr2:54950200-54952400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:54950200-54952400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr2:54950200-54952400	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr2:54950200-54952400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:54950200-54952400	Active TSS	Brain Anterior Caudate	brain
25	chr2:54950200-54952400	Active TSS	Ovary	ovary
26	chr2:54950200-54952400	Active TSS	NHDF-Ad	bronchial
27	chr2:54950200-54952600	Active TSS	Brain Hippocampus Middle	brain
28	chr2:54950200-54952600	Active TSS	Brain Substantia Nigra	brain
29	chr2:54950200-54952600	Active TSS	NHLF	lung
30	chr2:54950200-54953200	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:54950200-54953400	Active TSS	Brain Cingulate Gyrus	brain
32	chr2:54950200-54953600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:54950200-54954400	Active TSS	Brain Angular Gyrus	brain
34	chr2:54950400-54951800	Active TSS	Fetal Brain Male	brain
35	chr2:54950400-54954000	Active TSS	Fetal Brain Female	brain
36	chr2:54950600-54952200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:54950800-54951600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:54950800-54952800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr2:54950800-54953000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
40	chr2:54951000-54951600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
41	chr2:54951000-54951600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr2:54951000-54951600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr2:54951000-54951800	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:54951000-54951800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr2:54951000-54951800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr2:54951000-54951800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr2:54951000-54951800	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr2:54951000-54952000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
49	chr2:54951000-54952000	Flanking Active TSS	HMEC	breast
50	chr2:54951000-54952200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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