Variant report

Variant	rs10205410
Chromosome Location	chr2:54799599-54799600
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54782556..54791633-chr2:54796824..54803982,19	MCF-7	breast:
2	chr2:54796760..54799671-chr2:54800450..54802770,2	K562	blood:
3	chr2:54799047..54801001-chr2:54844688..54847061,2	MCF-7	breast:
4	chr2:54783962..54788714-chr2:54796833..54801765,9	K562	blood:
5	chr2:54759032..54761078-chr2:54799312..54800939,2	MCF-7	breast:
6	chr2:54793317..54796723-chr2:54797852..54801262,4	MCF-7	breast:
7	chr2:54797362..54799747-chr2:54810321..54813282,3	K562	blood:
8	chr2:54798938..54801134-chr2:54831623..54833818,2	K562	blood:
9	chr2:54781728..54792106-chr2:54796721..54808716,28	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10166844	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10169954	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10169975	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10170066	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10170355	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10176359	1.00[CHB][hapmap]
rs10176445	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs10182538	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10182836	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10183043	0.93[ASN][1000 genomes]
rs10183867	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10184128	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187338	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10188185	1.00[CHB][hapmap]
rs10188545	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10193692	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10204932	0.85[AFR][1000 genomes]
rs10206143	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10208225	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10210502	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10528	0.84[CHB][hapmap]
rs1137645	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11892236	1.00[CHB][hapmap]
rs11892443	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11896957	0.81[ASN][1000 genomes]
rs11898032	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11898033	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11902987	1.00[CHB][hapmap];0.82[JPT][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11904679	1.00[CHB][hapmap]
rs12713262	0.81[ASN][1000 genomes]
rs12713263	0.81[ASN][1000 genomes]
rs12713264	1.00[CHB][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713265	1.00[CHB][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713266	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713267	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713268	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713269	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713270	0.81[ASN][1000 genomes]
rs12713271	0.81[ASN][1000 genomes]
rs12713273	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs12713274	0.89[ASN][1000 genomes]
rs12987967	0.82[ASN][1000 genomes]
rs13021615	1.00[CHB][hapmap]
rs13386146	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391522	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13399656	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403284	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13407214	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13423873	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13432302	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17039558	1.00[CHB][hapmap]
rs17045939	1.00[CHB][hapmap]
rs17046097	0.83[EUR][1000 genomes]
rs17046108	0.84[CHB][hapmap]
rs17046257	1.00[CHB][hapmap]
rs2048370	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2229503	1.00[CHB][hapmap]
rs2271329	0.84[CHB][hapmap]
rs28581481	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3287	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34077590	0.93[ASN][1000 genomes]
rs34094680	0.87[ASN][1000 genomes]
rs34978408	0.81[ASN][1000 genomes]
rs354232	0.86[CHB][hapmap]
rs3739109	1.00[CHB][hapmap]
rs3796017	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796018	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796019	1.00[CHB][hapmap]
rs3796022	1.00[CHB][hapmap]
rs4261758	1.00[CHB][hapmap]
rs4319969	1.00[CHB][hapmap]
rs4346422	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4347868	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4358162	0.81[ASN][1000 genomes]
rs4374410	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4455200	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519566	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4577321	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4616509	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641979	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57281248	0.93[ASN][1000 genomes]
rs6545430	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6545435	1.00[CHB][hapmap]
rs6706263	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6721612	0.81[ASN][1000 genomes]
rs6724136	0.85[ASN][1000 genomes]
rs6730876	0.81[ASN][1000 genomes]
rs6734445	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs6734536	1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs6739140	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6740893	0.84[EUR][1000 genomes]
rs6749802	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7340302	1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424459	0.93[ASN][1000 genomes]
rs7556752	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7564719	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7569127	1.00[CHB][hapmap]
rs7584223	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7586066	0.97[ASN][1000 genomes]
rs7586311	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7591204	0.85[EUR][1000 genomes]
rs7591231	0.90[EUR][1000 genomes]
rs7599241	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602992	0.95[ASN][1000 genomes]
rs7608414	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs9677089	0.83[EUR][1000 genomes];0.85[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
rs10205410	EML6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54789800-54801400	Enhancers	Liver	Liver
2	chr2:54791200-54801200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr2:54793000-54799800	Enhancers	Stomach Mucosa	stomach
4	chr2:54794400-54804200	Weak transcription	Ovary	ovary
5	chr2:54795200-54799800	Enhancers	Fetal Intestine Large	intestine
6	chr2:54795200-54802200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:54795400-54801400	Enhancers	Fetal Thymus	thymus
8	chr2:54795600-54802400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr2:54795800-54800000	Enhancers	NHLF	lung
10	chr2:54795800-54801200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:54795800-54801800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr2:54795800-54801800	Enhancers	Fetal Kidney	kidney
13	chr2:54795800-54802400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:54795800-54803000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr2:54795800-54803200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:54795800-54803400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:54795800-54807000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:54795800-54807600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr2:54796000-54801200	Enhancers	Thymus	Thymus
20	chr2:54796000-54801600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:54796000-54801600	Enhancers	Brain Substantia Nigra	brain
22	chr2:54796000-54801800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:54796000-54802000	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:54796000-54802000	Enhancers	Fetal Lung	lung
25	chr2:54796000-54802200	Enhancers	HSMMtube	muscle
26	chr2:54796000-54802400	Enhancers	Brain Hippocampus Middle	brain
27	chr2:54796000-54802600	Enhancers	HMEC	breast
28	chr2:54796000-54802800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:54796000-54804400	Enhancers	Adipose Nuclei	Adipose
30	chr2:54796000-54807600	Enhancers	Brain Angular Gyrus	brain
31	chr2:54796200-54800400	Enhancers	Fetal Muscle Leg	muscle
32	chr2:54796200-54801400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:54796200-54801400	Enhancers	Placenta	Placenta
34	chr2:54796200-54801600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr2:54796200-54801800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr2:54796200-54806200	Enhancers	Right Atrium	heart
37	chr2:54796200-54806400	Enhancers	Brain Anterior Caudate	brain
38	chr2:54796200-54806800	Enhancers	Pancreas	Pancrea
39	chr2:54796400-54802200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:54796400-54803600	Enhancers	Placenta Amnion	Placenta Amnion
41	chr2:54796400-54808800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:54796600-54799800	Enhancers	Fetal Intestine Small	intestine
43	chr2:54796600-54801200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:54796600-54802200	Flanking Active TSS	GM12878-XiMat	blood
45	chr2:54796800-54799600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:54796800-54800600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:54796800-54800600	Enhancers	Fetal Stomach	stomach
48	chr2:54796800-54802200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr2:54796800-54802800	Enhancers	K562	blood
50	chr2:54796800-54803200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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