Variant report

Variant	rs10176359
Chromosome Location	chr2:54845698-54845699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54799047..54801001-chr2:54844688..54847061,2	MCF-7	breast:
2	chr2:54837203..54842761-chr2:54843020..54847377,6	K562	blood:
3	chr2:54843777..54846738-chr2:54866756..54869146,2	MCF-7	breast:
4	chr2:54844139..54846424-chr2:198364011..198365703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144381	Chromatin interaction
ENSG00000270757	Chromatin interaction
ENSG00000115541	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10169439	1.00[CEU][hapmap]
rs10170355	1.00[CHB][hapmap]
rs10176445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10182836	1.00[CHB][hapmap]
rs10183043	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10183867	1.00[CHB][hapmap]
rs10184128	1.00[CHB][hapmap]
rs10188185	1.00[CHB][hapmap]
rs10193692	1.00[CHB][hapmap]
rs10205410	1.00[CHB][hapmap]
rs10206143	1.00[CHB][hapmap]
rs10210502	0.86[EUR][1000 genomes]
rs10528	0.84[CEU][hapmap];0.88[CHB][hapmap];0.91[EUR][1000 genomes]
rs1137645	1.00[CHB][hapmap]
rs11555856	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892236	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892443	1.00[CHB][hapmap]
rs11896957	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11902659	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11902987	1.00[CHB][hapmap]
rs11904679	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[EUR][1000 genomes]
rs12713262	0.83[EUR][1000 genomes]
rs12713263	0.83[EUR][1000 genomes]
rs12713264	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12713265	1.00[CHB][hapmap]
rs12713268	1.00[CHB][hapmap]
rs12713269	1.00[CHB][hapmap]
rs12713270	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713271	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713272	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713273	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713274	0.82[ASN][1000 genomes]
rs12987967	0.80[EUR][1000 genomes]
rs13004944	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13021606	0.92[EUR][1000 genomes]
rs13021615	0.88[CHB][hapmap]
rs13386146	1.00[CHB][hapmap]
rs13391522	1.00[CHB][hapmap]
rs13391803	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13399656	1.00[CHB][hapmap]
rs13403284	1.00[CHB][hapmap]
rs13408295	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13428703	0.92[CEU][hapmap]
rs17039558	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs17045939	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs17046036	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046061	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046067	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046077	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs17046108	0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs17046257	1.00[CHB][hapmap]
rs2048370	0.88[CHB][hapmap]
rs2229503	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271329	0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs2971886	0.83[AFR][1000 genomes]
rs3287	1.00[CHB][hapmap]
rs34077590	0.82[EUR][1000 genomes]
rs34094680	0.82[EUR][1000 genomes]
rs34311770	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34978408	0.82[EUR][1000 genomes]
rs354232	0.89[CHB][hapmap]
rs35619551	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3739109	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs3796019	1.00[CHB][hapmap]
rs3796022	0.89[CHB][hapmap]
rs4261758	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs4319969	0.89[CHB][hapmap]
rs4346422	1.00[CHB][hapmap]
rs4358162	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4374410	0.81[ASN][1000 genomes]
rs4455200	1.00[CHB][hapmap]
rs4519566	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4577321	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57281248	0.82[EUR][1000 genomes]
rs58419243	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545430	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs6545435	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545440	0.86[CEU][hapmap]
rs6706263	1.00[CHB][hapmap]
rs67079536	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6708082	0.92[CEU][hapmap]
rs6721612	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724136	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67244067	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6730876	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6734445	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs6734536	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6740893	0.91[ASN][1000 genomes]
rs6741053	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6752720	0.92[CEU][hapmap]
rs6753004	0.86[CEU][hapmap]
rs72806653	0.83[EUR][1000 genomes]
rs7340302	1.00[CHB][hapmap]
rs7424459	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7556752	1.00[CHB][hapmap]
rs7569127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582640	0.86[CEU][hapmap]
rs7584223	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7586066	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7599241	1.00[CHB][hapmap]
rs7602992	0.83[EUR][1000 genomes]
rs7608414	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.96[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
rs10176359	EML6	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54829800-54859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:54838800-54845800	Strong transcription	Primary B cells from cord blood	blood
3	chr2:54838800-54845800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:54838800-54846200	Enhancers	Right Atrium	heart
5	chr2:54838800-54848800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:54838800-54860200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:54839000-54846800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:54839000-54848200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr2:54839000-54864200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:54839200-54845800	Strong transcription	Colonic Mucosa	Colon
12	chr2:54839200-54846800	Genic enhancers	Liver	Liver
13	chr2:54839200-54848600	Genic enhancers	Left Ventricle	heart
14	chr2:54839200-54861800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:54839200-54866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:54839400-54853000	Strong transcription	Fetal Intestine Large	intestine
17	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:54839600-54852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:54839600-54862600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:54839800-54846800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:54839800-54847200	Genic enhancers	Fetal Lung	lung
22	chr2:54840800-54861400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:54841000-54861400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:54841000-54861400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:54841200-54846800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:54841200-54847200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:54841200-54861200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:54841600-54845800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:54841600-54852400	Strong transcription	HSMMtube	muscle
31	chr2:54841600-54856200	Strong transcription	Hela-S3	cervix
32	chr2:54841600-54857000	Strong transcription	HSMM	muscle
33	chr2:54841800-54845800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:54841800-54845800	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:54841800-54847000	Strong transcription	HMEC	breast
36	chr2:54841800-54857000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:54841800-54860000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:54841800-54860000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:54842000-54863600	Strong transcription	Fetal Brain Female	brain
40	chr2:54842200-54845800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:54842400-54845800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr2:54842400-54846200	Genic enhancers	Right Ventricle	heart
43	chr2:54842400-54856800	Strong transcription	NH-A	brain
44	chr2:54842400-54861400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:54842400-54862800	Strong transcription	NHEK	skin
46	chr2:54842600-54845800	Genic enhancers	Stomach Smooth Muscle	stomach
47	chr2:54842600-54845800	Genic enhancers	HepG2	liver
48	chr2:54842600-54846800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:54842600-54861000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:54842600-54892000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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