Variant report

Variant	rs61126015
Chromosome Location	chr2:54780203-54780204
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	chr2:54779914..54782319-chr2:54782662..54788670,5	MCF-7	breast:
2	chr2:54771500..54773380-chr2:54779555..54782261,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10210502	0.82[EUR][1000 genomes]
rs10528	0.85[EUR][1000 genomes]
rs11555856	0.89[EUR][1000 genomes]
rs11883910	0.81[EUR][1000 genomes]
rs11892236	0.83[EUR][1000 genomes]
rs11896957	0.85[EUR][1000 genomes]
rs11904679	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12713262	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713263	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713270	0.82[EUR][1000 genomes]
rs12713271	0.82[EUR][1000 genomes]
rs12713273	0.82[EUR][1000 genomes]
rs12987967	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13006815	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13021606	0.85[EUR][1000 genomes]
rs13021615	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13036147	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13391803	0.88[EUR][1000 genomes]
rs17039558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045939	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17046061	0.83[EUR][1000 genomes]
rs17046067	0.83[EUR][1000 genomes]
rs2229503	0.85[EUR][1000 genomes]
rs34077590	0.90[EUR][1000 genomes]
rs34094680	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34263579	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34308676	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34311770	0.83[EUR][1000 genomes]
rs34429083	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34978408	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35619551	0.82[EUR][1000 genomes]
rs36018286	0.88[EUR][1000 genomes]
rs3796022	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4261758	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4319969	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4358162	0.82[EUR][1000 genomes]
rs4519566	0.83[EUR][1000 genomes]
rs45487791	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4577321	0.83[EUR][1000 genomes]
rs57281248	0.90[EUR][1000 genomes]
rs58419243	0.83[EUR][1000 genomes]
rs6545430	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545435	0.81[EUR][1000 genomes]
rs66693131	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67079536	0.86[EUR][1000 genomes]
rs6721612	0.85[EUR][1000 genomes]
rs67244067	0.80[EUR][1000 genomes]
rs6730876	0.85[EUR][1000 genomes]
rs6734445	0.86[EUR][1000 genomes]
rs6734536	0.90[EUR][1000 genomes]
rs6741053	0.81[EUR][1000 genomes]
rs7424459	0.86[EUR][1000 genomes]
rs7584223	0.83[EUR][1000 genomes]
rs7586066	0.88[EUR][1000 genomes]
rs7602992	0.84[EUR][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
rs61126015	EML6	cis	Thyroid	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:54773800-54782200	Weak transcription	Ovary	ovary
7	chr2:54774000-54782400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:54774000-54782400	Weak transcription	Osteobl	bone
9	chr2:54774800-54781800	Weak transcription	Liver	Liver
10	chr2:54774800-54782400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:54775800-54780600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr2:54775800-54782400	Weak transcription	HSMM	muscle
13	chr2:54777000-54782000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:54777200-54783600	Weak transcription	Fetal Stomach	stomach
15	chr2:54777600-54780800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:54777600-54782000	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:54777600-54782200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:54777600-54782800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:54777600-54783600	Weak transcription	Brain Germinal Matrix	brain
20	chr2:54777600-54784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:54777600-54784800	Weak transcription	Aorta	Aorta
22	chr2:54777800-54780400	Weak transcription	Adipose Nuclei	Adipose
23	chr2:54777800-54782200	Weak transcription	Gastric	stomach
24	chr2:54777800-54782600	Weak transcription	Fetal Kidney	kidney
25	chr2:54777800-54784200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:54778000-54780400	Weak transcription	HSMMtube	muscle
27	chr2:54778000-54780600	Enhancers	Spleen	Spleen
28	chr2:54778000-54782400	Weak transcription	NHLF	lung
29	chr2:54778000-54783400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:54778000-54784200	Weak transcription	Fetal Brain Male	brain
31	chr2:54778200-54783000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:54778200-54783400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:54778400-54780400	Weak transcription	Brain Substantia Nigra	brain
34	chr2:54778600-54781000	Weak transcription	A549	lung
35	chr2:54778600-54781200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:54778600-54781800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:54778600-54781800	Weak transcription	Placenta	Placenta
38	chr2:54778600-54782400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:54778600-54782600	Weak transcription	Esophagus	oesophagus
40	chr2:54778600-54784000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:54778800-54780400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:54778800-54780400	Weak transcription	Fetal Thymus	thymus
43	chr2:54778800-54780600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:54778800-54780800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:54778800-54780800	Enhancers	Fetal Heart	heart
46	chr2:54778800-54781000	Weak transcription	Right Atrium	heart
47	chr2:54778800-54781400	Weak transcription	Psoas Muscle	Psoas
48	chr2:54778800-54781800	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:54778800-54782200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:54778800-54782200	Weak transcription	HMEC	breast

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