Variant report

Variant	rs4519562
Chromosome Location	chr2:54841209-54841210
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	chr2:54837203..54842761-chr2:54843020..54847377,6	K562	blood:
2	chr2:54815292..54817560-chr2:54840163..54841990,2	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10165490	1.00[YRI][hapmap]
rs10180713	0.95[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1047499	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11885703	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11892788	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11898012	1.00[YRI][hapmap]
rs12104998	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs12105792	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12467581	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468469	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12617036	0.85[EUR][1000 genomes]
rs12624153	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12713260	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13016942	0.86[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13399435	1.00[YRI][hapmap]
rs1367295	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs1510611	0.86[JPT][hapmap]
rs1541854	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168506	0.82[EUR][1000 genomes]
rs171350	0.84[EUR][1000 genomes]
rs17344072	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs17521078	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1864493	0.86[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2048371	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271322	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292356	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2292357	0.92[EUR][1000 genomes]
rs2931463	0.87[EUR][1000 genomes]
rs2931464	0.87[EUR][1000 genomes]
rs2941583	0.88[EUR][1000 genomes]
rs2941586	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2941587	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2941591	0.88[EUR][1000 genomes]
rs2941595	0.95[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2971875	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2971877	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2971879	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2971883	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2971887	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3106204	0.88[EUR][1000 genomes]
rs354213	0.86[EUR][1000 genomes]
rs354226	0.83[EUR][1000 genomes]
rs354228	0.85[EUR][1000 genomes]
rs354231	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs3796014	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4233952	0.81[EUR][1000 genomes]
rs4444573	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4455199	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4592889	0.87[EUR][1000 genomes]
rs4671221	0.83[EUR][1000 genomes]
rs4671222	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4671225	0.82[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4671226	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4671945	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4671946	0.85[EUR][1000 genomes]
rs4671947	0.85[EUR][1000 genomes]
rs4671949	0.87[EUR][1000 genomes]
rs4671951	0.86[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs4671955	0.84[EUR][1000 genomes]
rs4671956	0.86[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4671960	0.95[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4671961	0.95[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4990319	0.85[EUR][1000 genomes]
rs6545411	0.81[EUR][1000 genomes]
rs6545413	0.81[EUR][1000 genomes]
rs6545414	0.81[EUR][1000 genomes]
rs6545415	0.81[EUR][1000 genomes]
rs6545418	0.82[EUR][1000 genomes]
rs6545419	0.86[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6545427	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6545429	0.84[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6545434	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704769	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6706372	1.00[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6724590	0.82[EUR][1000 genomes]
rs6729826	0.86[EUR][1000 genomes]
rs6731661	0.95[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6732949	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6734658	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6735813	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6742607	0.80[EUR][1000 genomes]
rs6746016	1.00[YRI][hapmap]
rs6746306	0.82[EUR][1000 genomes]
rs6748816	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6760298	0.86[JPT][hapmap]
rs6761369	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6761398	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7558950	0.87[EUR][1000 genomes]
rs7563706	0.82[EUR][1000 genomes]
rs7589236	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7598568	0.96[ASN][1000 genomes]
rs7607451	1.00[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907135	0.95[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][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
rs4519562	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	chr2:54832400-54843400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54832400-54843800	Weak transcription	Brain Germinal Matrix	brain
4	chr2:54833400-54843400	Weak transcription	Fetal Brain Male	brain
5	chr2:54835400-54842600	Enhancers	Fetal Heart	heart
6	chr2:54836200-54842600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:54836800-54841400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:54837400-54841600	Genic enhancers	HepG2	liver
9	chr2:54837400-54842800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:54837800-54842600	Weak transcription	Small Intestine	intestine
11	chr2:54838200-54842600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:54838200-54842800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:54838200-54843400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:54838600-54845600	Strong transcription	GM12878-XiMat	blood
15	chr2:54838800-54843800	Genic enhancers	Brain Hippocampus Middle	brain
16	chr2:54838800-54845800	Strong transcription	Primary B cells from cord blood	blood
17	chr2:54838800-54845800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:54838800-54846200	Enhancers	Right Atrium	heart
19	chr2:54838800-54848800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:54838800-54860200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:54839000-54846800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:54839000-54848200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:54839000-54864200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:54839200-54841600	Genic enhancers	Adipose Nuclei	Adipose
26	chr2:54839200-54841600	Enhancers	Psoas Muscle	Psoas
27	chr2:54839200-54841600	Genic enhancers	HSMM	muscle
28	chr2:54839200-54841800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:54839200-54841800	Genic enhancers	Lung	lung
30	chr2:54839200-54841800	Genic enhancers	Right Ventricle	heart
31	chr2:54839200-54841800	Genic enhancers	Spleen	Spleen
32	chr2:54839200-54842200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:54839200-54842800	Strong transcription	Primary T cells from cord blood	blood
34	chr2:54839200-54843200	Genic enhancers	Brain Anterior Caudate	brain
35	chr2:54839200-54843200	Strong transcription	Fetal Intestine Small	intestine
36	chr2:54839200-54844600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:54839200-54845000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:54839200-54845200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr2:54839200-54845200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:54839200-54845200	Strong transcription	Fetal Stomach	stomach
41	chr2:54839200-54845400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr2:54839200-54845400	Strong transcription	Thymus	Thymus
43	chr2:54839200-54845600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:54839200-54845600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:54839200-54845600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:54839200-54845800	Strong transcription	Colonic Mucosa	Colon
47	chr2:54839200-54846800	Genic enhancers	Liver	Liver
48	chr2:54839200-54848600	Genic enhancers	Left Ventricle	heart
49	chr2:54839200-54861800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:54839200-54866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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