Variant report

Variant	rs2583395
Chromosome Location	chr4:102241741-102241742
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10007902	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs10017730	0.80[EUR][1000 genomes]
rs1031033	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1031034	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1031035	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10433980	0.80[EUR][1000 genomes]
rs10433981	0.82[EUR][1000 genomes]
rs10433982	0.82[EUR][1000 genomes]
rs13109704	0.82[EUR][1000 genomes]
rs13135441	0.80[EUR][1000 genomes]
rs1348161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441433	0.95[JPT][hapmap]
rs1476159	0.83[EUR][1000 genomes]
rs1530259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549513	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs1549515	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs1549516	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs1822168	0.80[EUR][1000 genomes]
rs1822169	0.80[EUR][1000 genomes]
rs2044043	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2583385	0.83[EUR][1000 genomes]
rs2583386	0.83[EUR][1000 genomes]
rs2583387	0.81[EUR][1000 genomes]
rs2583389	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2583391	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2583394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583397	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583399	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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583400	0.90[JPT][hapmap]
rs2583401	0.86[JPT][hapmap]
rs2583402	0.81[JPT][hapmap]
rs2583406	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2850326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850328	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850329	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850330	0.90[EUR][1000 genomes]
rs2850331	0.90[EUR][1000 genomes]
rs2850332	0.91[JPT][hapmap]
rs2850333	0.83[EUR][1000 genomes]
rs2850334	0.83[EUR][1000 genomes]
rs2850344	0.91[JPT][hapmap]
rs2850350	0.86[JPT][hapmap]
rs2850351	0.91[JPT][hapmap]
rs2850354	0.91[JPT][hapmap]
rs2850355	0.95[JPT][hapmap]
rs2850356	0.95[JPT][hapmap]
rs2850357	0.82[ASN][1000 genomes]
rs2850366	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850368	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850369	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850372	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850963	0.91[JPT][hapmap]
rs2850969	0.91[JPT][hapmap]
rs2850974	0.91[JPT][hapmap]
rs2850976	0.91[JPT][hapmap]
rs28664200	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4452435	0.96[CEU][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4574415	0.83[EUR][1000 genomes]
rs4698957	0.80[EUR][1000 genomes]
rs4699209	0.81[EUR][1000 genomes]
rs4699210	0.82[EUR][1000 genomes]
rs4699211	0.82[EUR][1000 genomes]
rs4699212	0.80[EUR][1000 genomes]
rs4699214	0.80[EUR][1000 genomes]
rs6532928	0.80[EUR][1000 genomes]
rs6816400	0.80[EUR][1000 genomes]
rs6824603	0.80[EUR][1000 genomes]
rs6845368	0.82[EUR][1000 genomes]
rs6846097	0.82[EUR][1000 genomes]
rs6852377	0.82[EUR][1000 genomes]
rs6856370	0.80[EUR][1000 genomes]
rs755961	0.91[JPT][hapmap]
rs7668224	0.82[EUR][1000 genomes]
rs7687487	0.82[EUR][1000 genomes]
rs920559	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2583395	AP001816.1	cis	Whole Blood	GTEx
rs2583395	EIF4E	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102228200-102249400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:102228200-102250400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:102228600-102241800	Weak transcription	HSMM	muscle
4	chr4:102228600-102247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:102230600-102242600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:102236400-102241800	Weak transcription	NHEK	skin
7	chr4:102237400-102242600	Weak transcription	Primary B cells from cord blood	blood
8	chr4:102237400-102243600	Weak transcription	Psoas Muscle	Psoas
9	chr4:102237400-102247200	Weak transcription	Primary T cells from cord blood	blood
10	chr4:102237600-102243400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr4:102238400-102244400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:102238600-102241800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:102239200-102241800	Weak transcription	Brain Angular Gyrus	brain
14	chr4:102240600-102242000	Weak transcription	Brain Anterior Caudate	brain
15	chr4:102241400-102242000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:102241400-102243600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr4:102241600-102241800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr4:102241600-102242000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:102241600-102242000	Enhancers	Small Intestine	intestine
20	chr4:102241600-102242200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:102241600-102242400	Enhancers	Liver	Liver
22	chr4:102241600-102242600	Enhancers	Adipose Nuclei	Adipose
23	chr4:102241600-102243200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:102241600-102243600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:102241600-102243800	Enhancers	Ovary	ovary

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