Variant report

Variant	rs6545418
Chromosome Location	chr2:54737222-54737223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54735530..54737587-chr2:54805600..54807327,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10180713	0.81[EUR][1000 genomes]
rs11892788	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11898012	0.81[ASN][1000 genomes]
rs12104998	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12105792	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12467581	0.82[EUR][1000 genomes]
rs12468469	0.83[EUR][1000 genomes]
rs12617036	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713260	0.83[EUR][1000 genomes]
rs13016942	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13399435	0.82[ASN][1000 genomes]
rs1367295	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1541854	0.83[EUR][1000 genomes]
rs17344044	0.80[ASN][1000 genomes]
rs17344072	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17521078	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864493	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2941595	0.82[EUR][1000 genomes]
rs2971887	0.80[EUR][1000 genomes]
rs3796014	0.82[EUR][1000 genomes]
rs4233952	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4444573	0.83[EUR][1000 genomes]
rs4455199	0.83[EUR][1000 genomes]
rs4514917	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4519562	0.82[EUR][1000 genomes]
rs4592889	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671221	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671222	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671225	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671226	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4671945	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671946	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671947	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671949	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671951	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671954	0.80[ASN][1000 genomes]
rs4671955	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4671956	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4990319	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545411	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545413	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545414	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545415	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545419	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545420	0.82[EUR][1000 genomes]
rs6545427	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545429	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545434	0.83[EUR][1000 genomes]
rs6704769	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6706372	0.83[EUR][1000 genomes]
rs6724590	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6729826	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6731661	0.83[EUR][1000 genomes]
rs6732949	0.83[EUR][1000 genomes]
rs6734658	0.83[EUR][1000 genomes]
rs6735813	0.82[EUR][1000 genomes]
rs6742607	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6746016	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6746306	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6748816	0.82[EUR][1000 genomes]
rs6761369	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6761398	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558950	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7563706	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7589236	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7607451	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545418	EML6	cis	Thyroid	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54725200-54737600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:54726400-54740000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:54726400-54740000	Weak transcription	Pancreas	Pancrea
5	chr2:54727600-54737800	Weak transcription	A549	lung
6	chr2:54728000-54737400	Weak transcription	HSMM	muscle
7	chr2:54730000-54739400	Weak transcription	Fetal Brain Female	brain
8	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:54730600-54739000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:54730600-54739200	Weak transcription	Spleen	Spleen
11	chr2:54730600-54739400	Weak transcription	HepG2	liver
12	chr2:54730600-54740000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:54730800-54738600	Enhancers	Fetal Lung	lung
14	chr2:54731200-54737400	Weak transcription	Fetal Stomach	stomach
15	chr2:54732400-54737400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:54732600-54737400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:54732600-54738200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:54732800-54737400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:54732800-54737400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:54732800-54737600	Weak transcription	NHLF	lung
21	chr2:54732800-54740000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
24	chr2:54733600-54737400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:54733600-54747000	Weak transcription	Gastric	stomach
26	chr2:54733800-54742200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:54734600-54738400	Enhancers	Fetal Heart	heart
28	chr2:54734600-54740800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr2:54734800-54737400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:54735200-54738200	Enhancers	Right Atrium	heart
31	chr2:54735200-54740400	Enhancers	Left Ventricle	heart
32	chr2:54735400-54737800	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:54735400-54738200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:54735400-54738200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:54735400-54738200	Enhancers	Right Ventricle	heart
36	chr2:54735600-54738400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:54735600-54738400	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:54735600-54738400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:54735600-54738600	Enhancers	Adipose Nuclei	Adipose
40	chr2:54735600-54738600	Enhancers	Brain Anterior Caudate	brain
41	chr2:54735600-54740800	Enhancers	Brain Angular Gyrus	brain
42	chr2:54735800-54738200	Enhancers	Stomach Smooth Muscle	stomach
43	chr2:54735800-54740600	Enhancers	Brain Hippocampus Middle	brain
44	chr2:54735800-54741000	Enhancers	Brain Substantia Nigra	brain
45	chr2:54736200-54737400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:54736200-54738200	Enhancers	Psoas Muscle	Psoas
47	chr2:54736600-54738200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr2:54736600-54738400	Enhancers	HSMMtube	muscle
49	chr2:54736600-54740800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr2:54736800-54737400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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