Variant report

Variant	rs17046257
Chromosome Location	chr2:54949785-54949786
allele	A/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	GTF2F1	chr2:54949675-54950790	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:54949527-54950069	U87	brain:	n/a	n/a
4	POLR2A	chr2:54949535-54950069	U87	brain:	n/a	n/a
5	POLR2A	chr2:54949700-54950705	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr2:54949697-54950085	MCF10A-Er-Src	breast:	n/a	chr2:54949893-54949903 chr2:54949893-54949903 chr2:54949893-54949903
7	TBP	chr2:54949783-54950906	K562	blood:	n/a	n/a
8	POLR2A	chr2:54949717-54952029	Raji	blood:	n/a	n/a
9	RAD21	chr2:54949764-54951129	IMR90	lung:	n/a	n/a
10	MXI1	chr2:54949356-54954156	SK-N-SH	brain:	n/a	chr2:54949674-54949689
11	CEBPB	chr2:54949759-54950891	Hela-S3	cervix:	n/a	chr2:54949914-54949931 chr2:54949905-54949918
12	MYC	chr2:54949753-54950005	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr2:54949471-54951074	U87	brain:	n/a	n/a
14	MYBL2	chr2:54949779-54951665	HepG2	liver:	n/a	n/a
15	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
16	MAX	chr2:54949727-54951255	Hela-S3	cervix:	n/a	n/a
17	FOS	chr2:54949690-54950072	MCF10A-Er-Src	breast:	n/a	chr2:54949893-54949903 chr2:54949893-54949903 chr2:54949893-54949903
18	FOS	chr2:54949715-54950061	MCF10A-Er-Src	breast:	n/a	chr2:54949893-54949903 chr2:54949893-54949903 chr2:54949893-54949903
19	SMC3	chr2:54949772-54951580	Hela-S3	cervix:	n/a	chr2:54950012-54950019
20	CEBPB	chr2:54949719-54950464	IMR90	lung:	n/a	chr2:54949914-54949931 chr2:54949905-54949918
21	HCFC1	chr2:54949547-54951672	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr2:54949584-54951068	U87	brain:	n/a	n/a
23	SREBP1	chr2:54949596-54951061	GM12878	blood:	n/a	n/a
24	MBD4	chr2:54949636-54950619	HepG2	liver:	n/a	n/a
25	E2F4	chr2:54949651-54951116	MCF10A-Er-Src	breast:	n/a	chr2:54949703-54949712 chr2:54950781-54950792 chr2:54950557-54950572
26	POLR2A	chr2:54949557-54950675	MCF10A-Er-Src	breast:	n/a	n/a
27	MXI1	chr2:54949594-54952119	IMR90	lung:	n/a	chr2:54949674-54949689
28	POLR2A	chr2:54949736-54950942	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr2:54949630-54951264	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:54949765-54951371	Hela-S3	cervix:	n/a	n/a
31	SMARCC2	chr2:54949632-54951383	Hela-S3	cervix:	n/a	chr2:54950598-54950607
32	POLR2A	chr2:54949746-54950072	Hela-S3	cervix:	n/a	n/a
33	FOS	chr2:54949725-54950062	MCF10A-Er-Src	breast:	n/a	chr2:54949893-54949903 chr2:54949893-54949903 chr2:54949893-54949903
34	MYC	chr2:54949695-54950030	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54942542..54944647-chr2:54947416..54949799,3	K562	blood:
2	chr2:54785416..54786973-chr2:54949128..54950959,2	K562	blood:

Variant related genes	Relation type
EML6	TF binding region
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10169439	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs10170355	1.00[CHB][hapmap]
rs10175967	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10176359	1.00[CHB][hapmap]
rs10176445	1.00[CHB][hapmap]
rs10182836	1.00[CHB][hapmap]
rs10183867	1.00[CHB][hapmap]
rs10184128	1.00[CHB][hapmap]
rs10188185	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs10193692	1.00[CHB][hapmap]
rs10194108	0.89[EUR][1000 genomes]
rs10205410	1.00[CHB][hapmap]
rs10206143	1.00[CHB][hapmap]
rs10528	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs1137645	1.00[CHB][hapmap]
rs11883962	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11888644	0.91[EUR][1000 genomes]
rs11892236	1.00[CHB][hapmap]
rs11892443	1.00[CHB][hapmap]
rs11892703	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11902987	1.00[CHB][hapmap]
rs11904679	0.89[CHB][hapmap]
rs12713264	1.00[CHB][hapmap]
rs12713265	1.00[CHB][hapmap]
rs12713268	1.00[CHB][hapmap]
rs12713269	1.00[CHB][hapmap]
rs12713273	1.00[CHB][hapmap]
rs12713276	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13021615	0.88[CHB][hapmap]
rs13386146	1.00[CHB][hapmap]
rs13391522	1.00[CHB][hapmap]
rs13391803	1.00[CHB][hapmap]
rs13399656	1.00[CHB][hapmap]
rs13403284	1.00[CHB][hapmap]
rs13419761	0.84[EUR][1000 genomes]
rs13428703	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs17039558	0.89[CHB][hapmap]
rs17046077	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs17046108	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs2048370	0.93[CEU][hapmap];0.88[CHB][hapmap]
rs2229503	1.00[CHB][hapmap]
rs2271329	0.86[CEU][hapmap];0.88[CHB][hapmap]
rs2971888	0.85[YRI][hapmap]
rs3287	1.00[CHB][hapmap]
rs34272251	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34456795	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs354232	0.89[CHB][hapmap];0.90[ASN][1000 genomes]
rs3739109	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs3796019	1.00[CHB][hapmap]
rs3796022	0.89[CHB][hapmap]
rs4261758	0.89[CHB][hapmap]
rs4319969	0.89[CHB][hapmap]
rs4346422	1.00[CHB][hapmap]
rs4455200	1.00[CHB][hapmap]
rs58878579	0.85[EUR][1000 genomes]
rs6545430	1.00[CHB][hapmap]
rs6545435	1.00[CHB][hapmap]
rs6545440	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs6706263	1.00[CHB][hapmap]
rs6708082	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs6732751	0.85[EUR][1000 genomes]
rs6734445	1.00[CHB][hapmap]
rs6734536	1.00[CHB][hapmap]
rs6740110	0.92[EUR][1000 genomes]
rs6744586	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6752720	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6753004	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs67909358	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7340302	1.00[CHB][hapmap]
rs7556752	1.00[CHB][hapmap]
rs7569127	1.00[CHB][hapmap]
rs7582640	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs7584223	1.00[CHB][hapmap]
rs7599241	1.00[CHB][hapmap]
rs7608414	1.00[CHB][hapmap]
rs9917248	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17046257	EML6	cis	Thyroid	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54945200-54950000	Weak transcription	Right Atrium	heart
2	chr2:54948000-54949800	Weak transcription	Pancreas	Pancrea
3	chr2:54949400-54949800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:54949400-54949800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:54949400-54949800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:54949400-54949800	Enhancers	NHDF-Ad	bronchial
7	chr2:54949400-54950400	Flanking Active TSS	K562	blood
8	chr2:54949600-54949800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr2:54949600-54949800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:54949600-54949800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
11	chr2:54949600-54949800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr2:54949600-54949800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
13	chr2:54949600-54949800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:54949600-54949800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:54949600-54949800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:54949600-54949800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr2:54949600-54949800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:54949600-54949800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:54949600-54949800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:54949600-54949800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:54949600-54949800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:54949600-54949800	Enhancers	Brain Anterior Caudate	brain
23	chr2:54949600-54949800	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:54949600-54949800	Enhancers	Brain Hippocampus Middle	brain
25	chr2:54949600-54949800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr2:54949600-54949800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:54949600-54949800	Enhancers	Brain Substantia Nigra	brain
28	chr2:54949600-54949800	Active TSS	Colonic Mucosa	Colon
29	chr2:54949600-54949800	Enhancers	Colon Smooth Muscle	Colon
30	chr2:54949600-54949800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr2:54949600-54949800	Enhancers	Fetal Intestine Large	intestine
32	chr2:54949600-54949800	Enhancers	Fetal Intestine Small	intestine
33	chr2:54949600-54949800	Enhancers	Fetal Kidney	kidney
34	chr2:54949600-54949800	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr2:54949600-54949800	Enhancers	Fetal Thymus	thymus
36	chr2:54949600-54949800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr2:54949600-54949800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr2:54949600-54949800	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:54949600-54949800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:54949600-54949800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:54949600-54949800	Enhancers	Stomach Smooth Muscle	stomach
42	chr2:54949600-54949800	Active TSS	Thymus	Thymus
43	chr2:54949600-54949800	Enhancers	HMEC	breast
44	chr2:54949600-54949800	Enhancers	HSMM	muscle
45	chr2:54949600-54949800	Enhancers	HSMMtube	muscle
46	chr2:54949600-54949800	Enhancers	HUVEC	blood vessel
47	chr2:54949600-54949800	Enhancers	NH-A	brain
48	chr2:54949600-54949800	Enhancers	NHLF	lung
49	chr2:54949600-54950000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
50	chr2:54949600-54950000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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