Variant report

Variant	rs1336043
Chromosome Location	chr6:76192998-76192999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10806039	0.96[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs10943253	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12176377	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12199457	0.81[JPT][hapmap]
rs12202178	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12213227	0.86[JPT][hapmap]
rs1336044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414597	0.89[JPT][hapmap]
rs1932523	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2464434	0.94[AMR][1000 genomes]
rs2464435	0.88[AMR][1000 genomes]
rs2703662	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703665	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2703702	0.83[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes]
rs2703714	0.82[ASW][hapmap];0.86[CHB][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2808182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808183	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2808186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2808206	0.88[AMR][1000 genomes]
rs2808207	0.86[CHB][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes]
rs2951917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2951918	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2951919	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2951920	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951922	0.82[ASW][hapmap];0.86[CHB][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2951924	0.85[CHB][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2951925	0.86[CHB][hapmap];0.93[AMR][1000 genomes]
rs2951926	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2951929	0.85[CHB][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2951932	0.86[CHB][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2998365	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2998366	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2998367	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2998382	0.88[AMR][1000 genomes]
rs2998384	0.88[AMR][1000 genomes]
rs2998389	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2998390	0.88[AMR][1000 genomes]
rs2998391	0.93[AMR][1000 genomes]
rs2998392	0.88[AMR][1000 genomes]
rs2998393	0.83[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes]
rs2998394	0.81[CHB][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4594918	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs6937196	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9341520	0.92[AMR][1000 genomes]
rs9343290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447510	0.86[JPT][hapmap]
rs9885866	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
5	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv886182	chr6:76096230-76194007	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
10	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
11	nsv348407	chr6:76192830-76195714	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1336043	EEF1A1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76183000-76200800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:76187400-76194200	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr6:76187800-76196000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:76189400-76193000	Enhancers	HSMMtube	muscle
5	chr6:76189600-76201200	Weak transcription	Lung	lung
6	chr6:76190000-76193000	Enhancers	Fetal Heart	heart
7	chr6:76190000-76193400	Enhancers	NHLF	lung
8	chr6:76190200-76193200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:76190200-76193800	Enhancers	Colon Smooth Muscle	Colon
10	chr6:76190200-76195000	Enhancers	A549	lung
11	chr6:76190400-76193200	Enhancers	Rectal Smooth Muscle	rectum
12	chr6:76190400-76193600	Enhancers	Adipose Nuclei	Adipose
13	chr6:76191200-76194400	Enhancers	HUVEC	blood vessel
14	chr6:76191400-76197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:76191600-76193000	Weak transcription	Left Ventricle	heart
16	chr6:76191600-76193000	Weak transcription	Right Atrium	heart
17	chr6:76191600-76193400	Weak transcription	Aorta	Aorta
18	chr6:76191600-76193600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:76191600-76202200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:76192000-76193000	Weak transcription	Psoas Muscle	Psoas
21	chr6:76192000-76193200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:76192000-76193800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:76192000-76193800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:76192000-76193800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:76192000-76194200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:76192000-76194200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:76192000-76197000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:76192000-76197600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:76192000-76198000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:76192000-76201400	Weak transcription	GM12878-XiMat	blood
31	chr6:76192200-76193000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:76192200-76193800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:76192200-76197400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:76192400-76193000	Weak transcription	Right Ventricle	heart
35	chr6:76192400-76197400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:76192600-76197400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:76192800-76194600	Enhancers	Fetal Muscle Leg	muscle
38	chr6:76192800-76195000	Enhancers	Fetal Lung	lung
39	chr6:76192800-76196800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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