Variant report

Variant	rs13004944
Chromosome Location	chr2:54869281-54869282
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54864735..54867892-chr2:54868332..54870818,3	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10169439	0.89[CEU][hapmap]
rs10170355	1.00[CHB][hapmap]
rs10176359	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10176445	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10182836	1.00[CHB][hapmap]
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	0.81[EUR][1000 genomes]
rs10528	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1137645	1.00[CHB][hapmap]
rs11555856	0.90[EUR][1000 genomes]
rs11892236	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11892443	1.00[CHB][hapmap]
rs11892703	0.82[ASN][1000 genomes]
rs11896957	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11902659	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902987	1.00[CHB][hapmap]
rs11904679	0.83[CEU][hapmap];0.89[CHB][hapmap];0.84[EUR][1000 genomes]
rs12713264	1.00[CHB][hapmap]
rs12713265	1.00[CHB][hapmap]
rs12713268	1.00[CHB][hapmap]
rs12713269	1.00[CHB][hapmap]
rs12713270	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713271	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713272	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713273	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs12987967	0.82[EUR][1000 genomes]
rs13021606	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13021615	0.88[CHB][hapmap];1.00[YRI][hapmap]
rs13386146	1.00[CHB][hapmap]
rs13391522	1.00[CHB][hapmap]
rs13391803	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13399656	1.00[CHB][hapmap]
rs13403284	1.00[CHB][hapmap]
rs13408295	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428703	0.85[CEU][hapmap]
rs17039558	0.89[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs17045939	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs17046036	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046061	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046067	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046077	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17046108	0.85[CEU][hapmap];0.88[CHB][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17046257	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs2048370	0.88[CHB][hapmap]
rs2229503	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271329	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3287	1.00[CHB][hapmap]
rs34077590	0.84[EUR][1000 genomes]
rs34094680	0.83[EUR][1000 genomes]
rs34311770	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34978408	0.83[EUR][1000 genomes]
rs354232	0.89[CHB][hapmap]
rs35619551	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739109	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3796019	1.00[CHB][hapmap]
rs3796022	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4261758	0.89[CHB][hapmap];0.81[EUR][1000 genomes]
rs4319969	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4346422	1.00[CHB][hapmap]
rs4358162	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4455200	1.00[CHB][hapmap]
rs4519566	0.82[EUR][1000 genomes]
rs4577321	0.82[EUR][1000 genomes]
rs57281248	0.84[EUR][1000 genomes]
rs58419243	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545430	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs6545435	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706263	1.00[CHB][hapmap]
rs67079536	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6708082	0.85[CEU][hapmap]
rs6721612	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67244067	0.88[EUR][1000 genomes]
rs6730876	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6734445	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs6734536	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6741053	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752720	0.85[CEU][hapmap]
rs72806653	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7340302	1.00[CHB][hapmap]
rs7424459	0.85[EUR][1000 genomes]
rs7556752	1.00[CHB][hapmap]
rs7569127	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7584223	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7586066	0.87[EUR][1000 genomes]
rs7599241	1.00[CHB][hapmap]
rs7608414	1.00[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs13004944	EML6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54842600-54892000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54846400-54895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:54846400-54896600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:54846600-54898000	Strong transcription	Dnd41	blood
8	chr2:54846800-54895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:54848600-54892400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:54857000-54869400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:54857000-54883400	Strong transcription	Hela-S3	cervix
12	chr2:54859400-54873400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:54860400-54872800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:54861800-54898600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:54862200-54896600	Strong transcription	Primary hematopoietic stem cells	blood
16	chr2:54862400-54892800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:54862600-54869800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:54862600-54892400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:54862600-54892400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:54862600-54893400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:54862600-54898400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:54863000-54892000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr2:54863000-54892200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:54863000-54892400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:54863000-54895000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:54863000-54898600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:54863000-54899400	Strong transcription	Primary T cells from cord blood	blood
28	chr2:54863200-54886200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:54863600-54879400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr2:54863600-54897000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:54863800-54897400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:54863800-54898600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:54864200-54871400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:54864200-54885400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:54864200-54885400	Strong transcription	NH-A	brain
36	chr2:54864200-54893600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr2:54865200-54879400	Strong transcription	Thymus	Thymus
38	chr2:54865400-54892800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:54865400-54898400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:54865600-54869800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:54865800-54869600	Genic enhancers	Left Ventricle	heart
42	chr2:54865800-54870400	Genic enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:54865800-54898200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:54866000-54892800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:54866200-54884800	Strong transcription	Adipose Nuclei	Adipose
46	chr2:54866400-54870000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:54866400-54870200	Weak transcription	Fetal Brain Female	brain
48	chr2:54866400-54870400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr2:54866400-54871400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:54866400-54878400	Strong transcription	GM12878-XiMat	blood

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