Variant report

Variant	rs1541854
Chromosome Location	chr2:54828943-54828944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10180713	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1047499	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11885703	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11892788	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs12104998	0.81[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12105792	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs12467581	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12468469	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12617036	0.87[EUR][1000 genomes]
rs12624153	1.00[CHB][hapmap]
rs12713260	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13016942	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs1367295	0.81[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1510611	0.91[JPT][hapmap]
rs168506	0.81[EUR][1000 genomes]
rs171350	0.83[EUR][1000 genomes]
rs17344072	0.86[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17521078	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs1802889	1.00[YRI][hapmap]
rs1864493	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs2048371	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271322	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2292356	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2292357	0.91[EUR][1000 genomes]
rs2931463	0.86[EUR][1000 genomes]
rs2931464	0.86[EUR][1000 genomes]
rs2941583	0.86[EUR][1000 genomes]
rs2941586	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2941587	1.00[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2941591	0.86[EUR][1000 genomes]
rs2941595	0.95[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2971875	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2971877	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2971879	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2971883	0.87[EUR][1000 genomes]
rs2971887	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3106204	0.87[EUR][1000 genomes]
rs354213	0.84[EUR][1000 genomes]
rs354226	0.81[EUR][1000 genomes]
rs354228	0.84[EUR][1000 genomes]
rs354231	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs3796014	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4233952	0.82[EUR][1000 genomes]
rs4444573	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4455199	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4514917	0.80[EUR][1000 genomes]
rs4519562	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4592889	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4671221	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4671222	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs4671225	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs4671226	0.90[EUR][1000 genomes]
rs4671945	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs4671946	0.87[EUR][1000 genomes]
rs4671947	0.87[EUR][1000 genomes]
rs4671949	0.89[EUR][1000 genomes]
rs4671951	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4671955	0.85[EUR][1000 genomes]
rs4671956	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs4671960	0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671961	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4990319	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6545411	0.82[EUR][1000 genomes]
rs6545413	0.82[EUR][1000 genomes]
rs6545414	0.82[EUR][1000 genomes]
rs6545415	0.82[EUR][1000 genomes]
rs6545418	0.83[EUR][1000 genomes]
rs6545419	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6545427	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs6545429	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs6545434	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704769	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6706372	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6724590	0.83[EUR][1000 genomes]
rs6729826	0.87[EUR][1000 genomes]
rs6731661	0.95[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6732949	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6734658	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735813	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6742607	0.81[EUR][1000 genomes]
rs6746306	0.83[EUR][1000 genomes]
rs6748816	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6760298	0.91[JPT][hapmap]
rs6761369	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs6761398	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs7558950	0.89[EUR][1000 genomes]
rs7563706	0.83[EUR][1000 genomes]
rs7589236	0.89[EUR][1000 genomes]
rs7598568	0.99[ASN][1000 genomes]
rs7607451	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907135	0.95[CEU][hapmap];0.86[JPT][hapmap];0.90[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
rs1541854	EML6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:54822200-54833800	Genic enhancers	HepG2	liver
4	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
5	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
6	chr2:54822400-54834000	Enhancers	Right Atrium	heart
7	chr2:54822800-54831600	Genic enhancers	A549	lung
8	chr2:54823200-54831000	Genic enhancers	Fetal Intestine Large	intestine
9	chr2:54823800-54829400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:54824000-54829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:54824200-54829600	Enhancers	Fetal Heart	heart
12	chr2:54824200-54830600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:54824200-54833600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:54824400-54829200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:54824600-54834400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:54824800-54829600	Genic enhancers	Primary hematopoietic stem cells	blood
17	chr2:54824800-54834400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:54825000-54829200	Genic enhancers	HSMM	muscle
20	chr2:54825000-54829800	Weak transcription	Fetal Brain Male	brain
21	chr2:54825400-54829000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:54825800-54829600	Genic enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:54826000-54829600	Genic enhancers	Fetal Thymus	thymus
24	chr2:54826000-54831200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr2:54826200-54829000	Genic enhancers	NH-A	brain
26	chr2:54826400-54830200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:54826600-54832000	Genic enhancers	Fetal Intestine Small	intestine
28	chr2:54826800-54829600	Genic enhancers	Fetal Lung	lung
29	chr2:54826800-54830200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr2:54826800-54834400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:54827000-54829400	Enhancers	HSMMtube	muscle
32	chr2:54827000-54829600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:54827200-54830000	Genic enhancers	Primary B cells from peripheral blood	blood
34	chr2:54827200-54830400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:54827200-54832200	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:54827200-54833800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr2:54827200-54834000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:54827200-54839000	Weak transcription	Hela-S3	cervix
39	chr2:54827400-54829200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:54827400-54830200	Weak transcription	Thymus	Thymus
41	chr2:54827400-54831000	Enhancers	Rectal Smooth Muscle	rectum
42	chr2:54827400-54832000	Weak transcription	Brain Germinal Matrix	brain
43	chr2:54827400-54832000	Weak transcription	Fetal Brain Female	brain
44	chr2:54827600-54829000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:54827600-54829200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:54827600-54829200	Enhancers	Adipose Nuclei	Adipose
47	chr2:54827600-54829400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:54827600-54829400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:54827600-54829400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:54827600-54829400	Weak transcription	Esophagus	oesophagus

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