Variant report

Variant	rs28479319
Chromosome Location	chr7:5259199-5259200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5256728..5260872-chr7:5263140..5266583,5	K562	blood:
2	chr7:5256828..5260008-chr7:5263402..5265413,3	MCF-7	breast:
3	chr7:5242203..5244903-chr7:5258318..5259907,2	K562	blood:
4	chr7:5235801..5237554-chr7:5258054..5260873,2	MCF-7	breast:
5	chr7:5231544..5233195-chr7:5257262..5260176,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157954	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10261614	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10261752	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134489	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379233	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607283	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34213558	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41280675	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048056	1.00[ASN][1000 genomes]
rs7800499	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7800507	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7805752	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
3	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
4	nsv1031007	chr7:5101766-5262695	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv916396	chr7:5128917-5370805	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers 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 target site	20 gene(s)	inside rSNPs	diseases
6	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
7	nsv887390	chr7:5224407-5411296	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases
9	nsv830889	chr7:5248157-5427465	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv8034	chr7:5257953-5417973	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28479319	WIPI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5231400-5279800	Weak transcription	Fetal Brain Male	brain
2	chr7:5231800-5273400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:5234000-5274800	Weak transcription	Stomach Mucosa	stomach
4	chr7:5237400-5272600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:5237400-5273400	Strong transcription	Dnd41	blood
6	chr7:5239000-5267800	Strong transcription	Fetal Intestine Large	intestine
7	chr7:5239000-5270800	Strong transcription	Placenta	Placenta
8	chr7:5241000-5265600	Weak transcription	Psoas Muscle	Psoas
9	chr7:5246400-5271400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:5247800-5270000	Strong transcription	Primary T cells from cord blood	blood
11	chr7:5248400-5273200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:5248800-5267800	Strong transcription	Thymus	Thymus
13	chr7:5248800-5270600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:5248800-5272000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr7:5248800-5272200	Strong transcription	Fetal Muscle Leg	muscle
16	chr7:5248800-5272400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:5249000-5259600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr7:5249000-5259800	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr7:5249000-5260000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:5249000-5269200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:5249000-5269200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr7:5249000-5269600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr7:5249000-5269800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr7:5249000-5271200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr7:5249000-5272600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:5249000-5272800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:5249000-5272800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:5249000-5273000	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr7:5249000-5273200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr7:5249000-5273600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:5249000-5273600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:5249200-5259200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr7:5249200-5259200	Strong transcription	NHLF	lung
34	chr7:5249200-5259800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:5249200-5260400	Strong transcription	Lung	lung
36	chr7:5249200-5262000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:5249200-5269400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:5249200-5271800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:5249200-5272200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:5249200-5272400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:5249200-5272600	Strong transcription	Osteobl	bone
42	chr7:5249200-5272800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:5249200-5273000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr7:5249200-5273400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr7:5249200-5273400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:5249200-5273400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:5249200-5273400	Strong transcription	Fetal Stomach	stomach
48	chr7:5249200-5273400	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:5249200-5273600	Strong transcription	Fetal Intestine Small	intestine
50	chr7:5249400-5260600	Strong transcription	Left Ventricle	heart

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