Variant report

Variant	rs4616509
Chromosome Location	chr2:54807982-54807983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54806062..54808345-chr2:54823269..54826209,2	MCF-7	breast:
2	chr2:54785399..54787507-chr2:54807826..54810399,2	K562	blood:
3	chr2:54807406..54809056-chr2:54812643..54814659,2	MCF-7	breast:
4	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10166844	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10169954	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10169975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10170066	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170355	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176445	0.90[EUR][1000 genomes]
rs10182538	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183043	0.92[ASN][1000 genomes]
rs10183867	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184128	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10187338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188545	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10193692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205410	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10206143	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208225	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210502	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892443	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898032	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11898033	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11902987	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713264	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713265	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713266	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713267	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713273	0.89[ASN][1000 genomes]
rs12713274	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12987967	0.81[ASN][1000 genomes]
rs13386146	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391522	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391803	0.95[ASN][1000 genomes]
rs13399656	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13403284	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407214	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13423873	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13432302	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046097	0.88[EUR][1000 genomes]
rs28581481	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34077590	0.92[ASN][1000 genomes]
rs34094680	0.86[ASN][1000 genomes]
rs3796017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346422	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4347868	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4374410	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4455200	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4519566	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4577321	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4641979	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57281248	0.92[ASN][1000 genomes]
rs6545430	0.83[ASN][1000 genomes]
rs6706263	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724136	0.83[ASN][1000 genomes]
rs6734445	0.95[ASN][1000 genomes]
rs6734536	0.92[ASN][1000 genomes]
rs6739140	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6740893	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6749802	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7340302	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7424459	0.92[ASN][1000 genomes]
rs7556752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564719	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7584223	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586066	0.95[ASN][1000 genomes]
rs7586311	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591204	0.91[EUR][1000 genomes]
rs7591231	0.96[EUR][1000 genomes]
rs7599241	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7602992	0.94[ASN][1000 genomes]
rs7608414	0.90[EUR][1000 genomes]
rs9677089	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs4616509	EML6	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54796400-54808800	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr2:54796800-54810200	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr2:54796800-54810600	Enhancers	Small Intestine	intestine
4	chr2:54797400-54808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:54801600-54808600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:54801800-54811000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:54802000-54808400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:54802000-54816400	Enhancers	Liver	Liver
9	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
10	chr2:54802400-54808600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:54803600-54808400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:54804000-54808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:54804000-54809400	Enhancers	Fetal Kidney	kidney
14	chr2:54804000-54822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:54804200-54808600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:54804200-54809400	Enhancers	Thymus	Thymus
17	chr2:54804400-54808000	Enhancers	Fetal Stomach	stomach
18	chr2:54804600-54809800	Enhancers	Fetal Intestine Large	intestine
19	chr2:54804600-54814600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:54805000-54811000	Enhancers	Fetal Thymus	thymus
21	chr2:54805400-54810400	Enhancers	Primary B cells from peripheral blood	blood
22	chr2:54805400-54815800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:54805600-54810000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:54805600-54811800	Weak transcription	Ovary	ovary
26	chr2:54805600-54811800	Weak transcription	NHDF-Ad	bronchial
27	chr2:54805600-54819800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:54805800-54808400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:54806000-54808800	Weak transcription	Brain Germinal Matrix	brain
30	chr2:54806200-54809600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:54806200-54811800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:54806200-54813000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:54806400-54809200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:54806400-54809400	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr2:54806600-54808400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:54806600-54809600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr2:54806800-54808000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:54806800-54808000	Weak transcription	Lung	lung
39	chr2:54806800-54808000	Weak transcription	Pancreas	Pancrea
40	chr2:54806800-54808400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:54806800-54808400	Weak transcription	Gastric	stomach
42	chr2:54806800-54808400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:54806800-54808400	Weak transcription	Right Atrium	heart
44	chr2:54806800-54808400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:54806800-54808400	Weak transcription	Spleen	Spleen
46	chr2:54806800-54808800	Enhancers	Colonic Mucosa	Colon
47	chr2:54806800-54809000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:54806800-54809200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:54806800-54809800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr2:54806800-54811800	Weak transcription	Fetal Brain Male	brain

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