Variant report

Variant	rs2583398
Chromosome Location	chr4:102228696-102228697
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102226021..102228958-chr4:102267685..102270990,3	MCF-7	breast:
2	chr4:102226380..102228700-chr4:102233879..102237672,3	MCF-7	breast:
3	chr4:102228684..102230512-chr4:102715753..102717632,2	K562	blood:
4	chr4:102129139..102132021-chr4:102226843..102229507,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254531	Chromatin interaction
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10007902	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs1031033	1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1031034	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1031035	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13116679	0.83[ASW][hapmap]
rs1348161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441433	0.95[JPT][hapmap]
rs1530259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549513	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs1549515	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs1549516	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs2044043	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2583387	0.80[ASN][1000 genomes]
rs2583389	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2583391	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2583392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583394	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];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583395	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]
rs2583397	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583400	0.90[JPT][hapmap]
rs2583401	0.86[JPT][hapmap]
rs2583402	0.81[JPT][hapmap]
rs2583406	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2850326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2850328	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850329	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850330	0.84[EUR][1000 genomes]
rs2850331	0.84[EUR][1000 genomes]
rs2850332	0.91[JPT][hapmap]
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	0.83[ASN][1000 genomes]
rs2850366	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850368	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850369	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850371	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];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850372	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850963	0.91[JPT][hapmap]
rs2850969	0.91[JPT][hapmap]
rs2850974	0.91[JPT][hapmap]
rs2850976	0.91[JPT][hapmap]
rs28664200	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3804416	0.83[ASW][hapmap]
rs4452435	0.96[CEU][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs755961	0.91[JPT][hapmap]
rs920559	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2583398	AP001816.1	cis	Whole Blood	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102215000-102232600	Weak transcription	Pancreas	Pancrea
2	chr4:102215400-102236600	Weak transcription	Primary B cells from cord blood	blood
3	chr4:102222000-102232800	Weak transcription	Lung	lung
4	chr4:102225400-102228800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr4:102225600-102229200	Enhancers	Brain Anterior Caudate	brain
6	chr4:102225800-102229800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:102226000-102228800	Enhancers	A549	lung
8	chr4:102226000-102229200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:102226200-102228800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:102226200-102228800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:102226200-102229000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr4:102226200-102229000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr4:102226200-102229800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:102226400-102229200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:102226400-102232600	Weak transcription	Left Ventricle	heart
16	chr4:102226600-102229000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:102226600-102229000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:102226600-102229600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:102227000-102229800	Enhancers	NHLF	lung
20	chr4:102227200-102228800	Enhancers	Primary T cells from cord blood	blood
21	chr4:102227200-102229000	Enhancers	Primary B cells from peripheral blood	blood
22	chr4:102227200-102229000	Flanking Active TSS	GM12878-XiMat	blood
23	chr4:102227200-102229200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr4:102227200-102229200	Enhancers	Colon Smooth Muscle	Colon
25	chr4:102227200-102230200	Enhancers	NHEK	skin
26	chr4:102227600-102228800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr4:102227600-102228800	Weak transcription	Gastric	stomach
28	chr4:102227600-102230200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:102227800-102228800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:102227800-102228800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:102227800-102228800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:102227800-102238200	Weak transcription	Right Ventricle	heart
33	chr4:102228000-102229400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:102228000-102229600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:102228000-102229600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:102228000-102229800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:102228000-102231000	Enhancers	Stomach Mucosa	stomach
38	chr4:102228200-102229000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:102228200-102229000	Enhancers	Osteobl	bone
40	chr4:102228200-102229400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:102228200-102229600	Weak transcription	Psoas Muscle	Psoas
42	chr4:102228200-102230000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:102228200-102230200	Enhancers	HMEC	breast
44	chr4:102228200-102231200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:102228200-102249400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:102228200-102250400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:102228400-102228800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr4:102228400-102229000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:102228400-102231000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr4:102228600-102229000	Enhancers	Pancreatic Islets	Pancreatic Islet

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