Variant report

Variant	rs13021615
Chromosome Location	chr2:54771323-54771324
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	STAT3	chr2:54771288-54771441	MCF10A-Er-Src	breast:	n/a	chr2:54771417-54771440
2	GATA3	chr2:54771277-54771563	SH-SY5Y	brain:	n/a	n/a
3	RCOR1	chr2:54771119-54771509	K562	blood:	n/a	n/a
4	RCOR1	chr2:54771216-54771480	K562	blood:	n/a	n/a
5	GATA2	chr2:54771224-54771536	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54767808..54771330-chr2:54771769..54776449,4	K562	blood:
2	chr2:54770128..54773516-chr2:54775238..54777528,3	MCF-7	breast:
3	chr2:54764232..54766337-chr2:54769153..54772806,3	K562	blood:

Variant related genes	Relation type
ENSG00000228108	TF binding region
ENSG00000234943	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10170355	0.88[CHB][hapmap]
rs10176359	0.88[CHB][hapmap]
rs10176445	0.88[CHB][hapmap]
rs10182836	0.88[CHB][hapmap]
rs10183867	0.88[CHB][hapmap]
rs10184128	0.88[CHB][hapmap]
rs10188185	0.85[CHB][hapmap]
rs10193692	0.86[CHB][hapmap]
rs10205410	1.00[CHB][hapmap]
rs10206143	0.88[CHB][hapmap]
rs10210502	0.80[EUR][1000 genomes]
rs10528	0.85[EUR][1000 genomes]
rs1137645	0.88[CHB][hapmap]
rs11555856	0.85[EUR][1000 genomes]
rs11883910	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11892236	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11892443	1.00[CHB][hapmap]
rs11896957	0.81[EUR][1000 genomes]
rs11902987	1.00[CHB][hapmap]
rs11904679	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713262	0.83[EUR][1000 genomes]
rs12713263	0.83[EUR][1000 genomes]
rs12713264	0.88[CHB][hapmap]
rs12713265	0.88[CHB][hapmap]
rs12713268	0.88[CHB][hapmap]
rs12713269	0.88[CHB][hapmap]
rs12713273	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs12987967	0.87[EUR][1000 genomes]
rs13006815	0.87[EUR][1000 genomes]
rs13021606	0.81[EUR][1000 genomes]
rs13036147	0.90[EUR][1000 genomes]
rs13386146	0.88[CHB][hapmap]
rs13391522	0.88[CHB][hapmap]
rs13391803	0.86[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs13399656	0.86[CHB][hapmap]
rs13403284	0.88[CHB][hapmap]
rs17039558	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045939	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[EUR][1000 genomes]
rs17046061	0.83[EUR][1000 genomes]
rs17046067	0.83[EUR][1000 genomes]
rs17046077	1.00[YRI][hapmap]
rs17046108	0.89[YRI][hapmap]
rs17046257	0.88[CHB][hapmap]
rs17343815	0.80[EUR][1000 genomes]
rs2229503	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2271329	1.00[YRI][hapmap]
rs3287	0.88[CHB][hapmap]
rs34077590	0.88[EUR][1000 genomes]
rs34094680	0.92[EUR][1000 genomes]
rs34263579	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34308676	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34311770	0.83[EUR][1000 genomes]
rs34429083	0.91[EUR][1000 genomes]
rs34978408	0.92[EUR][1000 genomes]
rs35619551	0.82[EUR][1000 genomes]
rs36018286	0.94[EUR][1000 genomes]
rs3739109	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs3796019	0.88[CHB][hapmap]
rs3796022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4261758	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4346422	0.88[CHB][hapmap]
rs4455200	0.86[CHB][hapmap]
rs4519566	0.82[EUR][1000 genomes]
rs45487791	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4577321	0.82[EUR][1000 genomes]
rs57281248	0.88[EUR][1000 genomes]
rs58419243	0.83[EUR][1000 genomes]
rs61126015	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545430	0.86[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs6545435	0.85[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs66693131	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6706263	0.86[CHB][hapmap]
rs67079536	0.86[EUR][1000 genomes]
rs6721612	0.81[EUR][1000 genomes]
rs6730876	0.81[EUR][1000 genomes]
rs6734445	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[EUR][1000 genomes]
rs6734536	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs7340302	0.88[CHB][hapmap]
rs7424459	0.84[EUR][1000 genomes]
rs7556752	0.88[CHB][hapmap]
rs7569127	0.88[CHB][hapmap]
rs7584223	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs7586066	0.86[EUR][1000 genomes]
rs7599241	0.88[CHB][hapmap]
rs7602992	0.82[EUR][1000 genomes]
rs7608414	0.88[CHB][hapmap]

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
rs13021615	EML6	cis	Thyroid	GTEx

Chromatin state (count:80 , 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	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
3	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
6	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:54761600-54773200	Weak transcription	Fetal Brain Male	brain
8	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:54762200-54772800	Weak transcription	Aorta	Aorta
10	chr2:54762200-54772800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:54762200-54773800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:54762400-54772600	Weak transcription	Liver	Liver
13	chr2:54762800-54772600	Weak transcription	NHDF-Ad	bronchial
14	chr2:54763000-54776000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:54763200-54772600	Weak transcription	NHLF	lung
16	chr2:54764000-54776800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:54764400-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:54764600-54772600	Weak transcription	Osteobl	bone
19	chr2:54765600-54774000	Weak transcription	Fetal Brain Female	brain
20	chr2:54766200-54772800	Weak transcription	Small Intestine	intestine
21	chr2:54767200-54771600	Enhancers	Brain Angular Gyrus	brain
22	chr2:54767200-54771600	Enhancers	Brain Hippocampus Middle	brain
23	chr2:54767400-54772600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:54767400-54772800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:54767800-54772600	Weak transcription	HUVEC	blood vessel
26	chr2:54767800-54772600	Weak transcription	NH-A	brain
27	chr2:54767800-54773000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:54768200-54772600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:54768400-54772800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:54768400-54773000	Weak transcription	Fetal Lung	lung
32	chr2:54768400-54773600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:54768400-54775800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:54768600-54772800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:54768800-54772800	Weak transcription	HSMM	muscle
36	chr2:54768800-54772800	Weak transcription	HSMMtube	muscle
37	chr2:54769200-54771600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:54769400-54772400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:54769600-54771600	Enhancers	Colon Smooth Muscle	Colon
40	chr2:54769800-54772600	Enhancers	HepG2	liver
41	chr2:54769800-54772800	Weak transcription	Spleen	Spleen
42	chr2:54769800-54775400	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:54769800-54775600	Weak transcription	Fetal Stomach	stomach
44	chr2:54769800-54777000	Weak transcription	Psoas Muscle	Psoas
45	chr2:54770000-54777400	Weak transcription	GM12878-XiMat	blood
46	chr2:54770200-54771800	Genic enhancers	A549	lung
47	chr2:54770200-54772600	Weak transcription	Fetal Heart	heart
48	chr2:54770400-54771400	Weak transcription	Esophagus	oesophagus
49	chr2:54770400-54771600	Enhancers	Fetal Kidney	kidney
50	chr2:54770400-54772600	Weak transcription	Brain Substantia Nigra	brain

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