Variant report

Variant	rs12713262
Chromosome Location	chr2:54789232-54789233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54767756..54770528-chr2:54788177..54790066,2	MCF-7	breast:
2	chr2:54786715..54789713-chr2:54890702..54893003,2	K562	blood:
3	chr2:54789199..54791941-chr2:54810651..54814148,3	K562	blood:
4	chr2:54749132..54757147-chr2:54784492..54789269,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228108	Chromatin interaction
ENSG00000237887	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10166844	0.82[ASN][1000 genomes]
rs10170355	0.80[EUR][1000 genomes]
rs10176359	0.83[EUR][1000 genomes]
rs10183043	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10184128	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10188545	0.81[ASN][1000 genomes]
rs10205410	0.81[ASN][1000 genomes]
rs10210502	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10528	0.84[EUR][1000 genomes]
rs11555856	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11892236	0.83[EUR][1000 genomes]
rs11896957	0.83[EUR][1000 genomes]
rs11898032	0.83[ASN][1000 genomes]
rs11898033	0.83[ASN][1000 genomes]
rs11902659	0.83[EUR][1000 genomes]
rs12713263	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713270	0.87[EUR][1000 genomes]
rs12713271	0.87[EUR][1000 genomes]
rs12713272	0.83[EUR][1000 genomes]
rs12713273	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12987967	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13021606	0.83[EUR][1000 genomes]
rs13021615	0.83[EUR][1000 genomes]
rs13386146	0.81[ASN][1000 genomes]
rs13391803	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13399656	0.81[ASN][1000 genomes]
rs13407214	0.81[ASN][1000 genomes]
rs13423873	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17039558	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17046061	0.83[EUR][1000 genomes]
rs17046067	0.83[EUR][1000 genomes]
rs2229503	0.84[EUR][1000 genomes]
rs34077590	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34094680	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34308676	0.86[EUR][1000 genomes]
rs34311770	0.83[EUR][1000 genomes]
rs34978408	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35619551	0.82[EUR][1000 genomes]
rs3796022	0.81[EUR][1000 genomes]
rs4261758	0.83[EUR][1000 genomes]
rs4346422	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4358162	0.87[EUR][1000 genomes]
rs4374410	0.84[ASN][1000 genomes]
rs4455200	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4519566	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577321	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57281248	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58419243	0.83[EUR][1000 genomes]
rs61126015	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545435	0.88[EUR][1000 genomes]
rs66693131	0.81[EUR][1000 genomes]
rs67079536	0.84[EUR][1000 genomes]
rs6721612	0.83[EUR][1000 genomes]
rs6724136	0.86[EUR][1000 genomes]
rs67244067	0.85[EUR][1000 genomes]
rs6730876	0.83[EUR][1000 genomes]
rs6734445	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6734536	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6739140	0.83[ASN][1000 genomes]
rs6749802	0.83[ASN][1000 genomes]
rs7340302	0.81[ASN][1000 genomes]
rs7424459	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7564719	0.81[ASN][1000 genomes]
rs7569127	0.83[EUR][1000 genomes]
rs7584223	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7586066	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7599241	0.81[ASN][1000 genomes]
rs7602992	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[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	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	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
rs12713262	EML6	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54784800-54789800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:54785000-54789400	Active TSS	GM12878-XiMat	blood
3	chr2:54786400-54790200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr2:54786400-54793200	Enhancers	Fetal Heart	heart
5	chr2:54787200-54789800	Active TSS	Fetal Stomach	stomach
6	chr2:54787600-54791400	Enhancers	Left Ventricle	heart
7	chr2:54787600-54791400	Weak transcription	Right Ventricle	heart
8	chr2:54787600-54791400	Weak transcription	Spleen	Spleen
9	chr2:54787600-54796800	Weak transcription	Aorta	Aorta
10	chr2:54787600-54797000	Weak transcription	Gastric	stomach
11	chr2:54787800-54790600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:54787800-54796200	Weak transcription	Esophagus	oesophagus
13	chr2:54787800-54797200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:54788000-54789400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:54788000-54791000	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:54788000-54791200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:54788000-54796000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:54788200-54790600	Enhancers	Fetal Lung	lung
19	chr2:54788200-54795000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:54788400-54789400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:54788400-54789400	Weak transcription	Fetal Brain Male	brain
22	chr2:54788400-54789600	Enhancers	Osteobl	bone
23	chr2:54788400-54789800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:54788400-54789800	Enhancers	Small Intestine	intestine
25	chr2:54788400-54790600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr2:54788400-54790600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr2:54788400-54791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:54788400-54797600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:54788600-54789400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:54788600-54789400	Weak transcription	Adipose Nuclei	Adipose
31	chr2:54788600-54789400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:54788600-54789600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr2:54788600-54789600	Enhancers	H9 Cell Line	embryonic stem cell
34	chr2:54788600-54789600	Enhancers	NHDF-Ad	bronchial
35	chr2:54788600-54789800	Weak transcription	Pancreas	Pancrea
36	chr2:54788600-54789800	Enhancers	Right Atrium	heart
37	chr2:54788600-54790000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:54788600-54790200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:54788600-54790600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:54788600-54791000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:54788600-54791200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr2:54788600-54791600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:54788600-54791600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:54788600-54791800	Enhancers	Stomach Mucosa	stomach
45	chr2:54788600-54792000	Enhancers	Fetal Thymus	thymus
46	chr2:54788600-54795200	Weak transcription	Placenta	Placenta
47	chr2:54788600-54796000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:54788600-54796200	Weak transcription	Colonic Mucosa	Colon
49	chr2:54788600-54796200	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:54788600-54796400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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