Variant report

Variant	rs6739140
Chromosome Location	chr2:54823502-54823503
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54823186..54826195-chr2:54832588..54835705,3	K562	blood:
2	chr2:54806062..54808345-chr2:54823269..54826209,2	MCF-7	breast:
3	chr2:54822318..54824059-chr2:54829758..54831616,2	MCF-7	breast:
4	chr2:54815707..54819448-chr2:54820160..54824681,7	K562	blood:
5	chr2:54815000..54820095-chr2:54820709..54825309,10	K562	blood:
6	chr2:54822853..54825212-chr2:54825239..54827897,2	MCF-7	breast:
7	chr2:54822696..54824811-chr2:54826177..54828033,3	K562	blood:
8	chr2:54816128..54819257-chr2:54823273..54825897,3	MCF-7	breast:

No data

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10166844	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10169954	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10169975	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10170066	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10170355	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10176445	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10182538	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10182836	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10183043	0.95[ASN][1000 genomes]
rs10183867	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10184128	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10187338	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10188545	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10193692	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10205410	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10206143	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208225	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10210502	0.94[ASN][1000 genomes]
rs1137645	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11892443	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11896957	0.82[ASN][1000 genomes]
rs11898032	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898033	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902987	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713262	0.83[ASN][1000 genomes]
rs12713263	0.83[ASN][1000 genomes]
rs12713264	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713265	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713266	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713267	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713268	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713269	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713270	0.82[ASN][1000 genomes]
rs12713271	0.82[ASN][1000 genomes]
rs12713273	0.92[ASN][1000 genomes]
rs12713274	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12987967	0.84[ASN][1000 genomes]
rs13386146	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13391522	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13391803	0.92[ASN][1000 genomes]
rs13399656	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13403284	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13407214	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13423873	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13432302	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17046097	0.90[EUR][1000 genomes]
rs28581481	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3287	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34077590	0.89[ASN][1000 genomes]
rs34094680	0.89[ASN][1000 genomes]
rs34978408	0.83[ASN][1000 genomes]
rs3796017	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796018	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4346422	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4347868	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4358162	0.82[ASN][1000 genomes]
rs4374410	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4455200	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4519566	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577321	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4616509	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4641979	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57281248	0.89[ASN][1000 genomes]
rs6545430	0.86[ASN][1000 genomes]
rs6706263	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721612	0.82[ASN][1000 genomes]
rs6724136	0.86[ASN][1000 genomes]
rs6730876	0.82[ASN][1000 genomes]
rs6734445	0.92[ASN][1000 genomes]
rs6734536	0.89[ASN][1000 genomes]
rs6740893	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6749802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340302	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7424459	0.95[ASN][1000 genomes]
rs7556752	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564719	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7584223	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7586066	0.92[ASN][1000 genomes]
rs7586311	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7591204	0.93[EUR][1000 genomes]
rs7591231	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7599241	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7602992	0.90[ASN][1000 genomes]
rs7608414	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9677089	0.85[EUR][1000 genomes];0.81[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
rs6739140	EML6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54807000-54826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:54809600-54825800	Weak transcription	Brain Germinal Matrix	brain
4	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:54817000-54825800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:54817000-54826200	Weak transcription	NHDF-Ad	bronchial
8	chr2:54817400-54825400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:54817600-54823600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:54817600-54825000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:54817600-54825600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:54817800-54825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:54817800-54826200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:54817800-54826200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:54818000-54824400	Weak transcription	HMEC	breast
16	chr2:54818000-54826200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:54820200-54823600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:54820600-54824200	Weak transcription	Fetal Brain Female	brain
19	chr2:54820600-54824600	Weak transcription	Fetal Brain Male	brain
20	chr2:54820800-54823600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:54820800-54826000	Weak transcription	Osteobl	bone
22	chr2:54820800-54826200	Weak transcription	Hela-S3	cervix
23	chr2:54821000-54824400	Weak transcription	NHEK	skin
24	chr2:54821200-54824800	Enhancers	Primary hematopoietic stem cells	blood
25	chr2:54821400-54823800	Weak transcription	HSMMtube	muscle
26	chr2:54821800-54823600	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr2:54822000-54823600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:54822200-54823600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:54822200-54826200	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:54822200-54827800	Genic enhancers	Fetal Muscle Leg	muscle
31	chr2:54822200-54828800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:54822200-54833800	Genic enhancers	HepG2	liver
33	chr2:54822400-54823600	Enhancers	Fetal Heart	heart
34	chr2:54822400-54823600	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr2:54822400-54823800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:54822400-54824000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:54822400-54824000	Genic enhancers	NHLF	lung
38	chr2:54822400-54824200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:54822400-54825200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr2:54822400-54825600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr2:54822400-54825600	Enhancers	Brain Substantia Nigra	brain
42	chr2:54822400-54825600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr2:54822400-54825800	Enhancers	Pancreas	Pancrea
44	chr2:54822400-54826000	Enhancers	Right Ventricle	heart
45	chr2:54822400-54826400	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr2:54822400-54827600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:54822400-54827800	Enhancers	Colon Smooth Muscle	Colon
48	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
49	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
50	chr2:54822400-54834000	Enhancers	Right Atrium	heart

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