Variant report

Variant	rs28545115
Chromosome Location	chr7:5262934-5262935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:5262736-5262956	K562	blood:	n/a	n/a
2	POLR2A	chr7:5262895-5263349	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:5262533-5263600	MCF-7	breast:	n/a	n/a
4	POLR2A	chr7:5262931-5263179	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:5262924-5262974	HMEC	breast:	n/a
2	chr7:5262924-5262974	HNPCEpiC	eye:	n/a
3	chr7:5262924-5262974	SK-N-SH	brain:	n/a
4	chr7:5262924-5262974	Jurkat	blood:	n/a
5	chr7:5262924-5262974	HepG2	liver:	n/a
6	chr7:5262924-5262974	HCPEpiC	choroid plexus:	n/a
7	chr7:5262924-5262974	ECC-1	luminal epithelium:	n/a
8	chr7:5262924-5262974	AG10803	skin:	n/a
9	chr7:5262924-5262974	H1-hESC	embryonic stem cell:	embryo
10	chr7:5262924-5262974	AG09319	gingival:	n/a
11	chr7:5262924-5262974	ovcar-3	ovarian:	n/a
12	chr7:5262924-5262974	RPTEC	kidney:	n/a
13	chr7:5262924-5262974	Hepatocyte	liver:	n/a
14	chr7:5262924-5262974	K562	blood:	n/a
15	chr7:5262924-5262974	CMK	blood:	n/a
16	chr7:5262924-5262974	PrEC	prostate:	n/a
17	chr7:5262924-5262974	LNCaP	prostate:	n/a
18	chr7:5262924-5262974	ProgFib	skin:	n/a
19	chr7:5262924-5262974	AG04450	lung:	fetal
20	chr7:5262924-5262974	Hela-S3	cervix:	n/a
21	chr7:5262924-5262974	GM19239	blood:	n/a
22	chr7:5262924-5262974	HAEpiC	amniotic membrane:	n/a
23	chr7:5262924-5262974	HL-60	blood:	n/a
24	chr7:5262924-5262974	HPAEpiC	pulmonary alveolar:	n/a
25	chr7:5262924-5262974	Caco-2	colon:	n/a
26	chr7:5262924-5262974	PFSK-1	brain:	n/a
27	chr7:5262924-5262974	NT2-D1	testis:	n/a
28	chr7:5262924-5262974	A549	lung:	n/a
29	chr7:5262924-5262974	HCT-116	colon:	n/a
30	chr7:5262924-5262974	GM12892	blood:	n/a
31	chr7:5262924-5262974	AG04449	skin:	fetal
32	chr7:5262924-5262974	AG09309	skin:	n/a
33	chr7:5262924-5262974	SK-N-MC	brain:	n/a
34	chr7:5262924-5262974	HEEpiC	esophagus:	n/a
35	chr7:5262924-5262974	HUVEC	blood vessel:	n/a
36	chr7:5262924-5262974	PANC-1	pancreas:	n/a
37	chr7:5262924-5262974	GM06990	blood:	n/a
38	chr7:5262924-5262974	HRPEpiC	eye:	n/a
39	chr7:5262924-5262974	SK-N-SH_RA	brain:	n/a
40	chr7:5262924-5262974	HEK293	kidney:	embryo
41	chr7:5262924-5262974	MCF-7	breast:	n/a
42	chr7:5262924-5262974	HCM	heart:	n/a
43	chr7:5262924-5262974	NB4	blood:	n/a
44	chr7:5262924-5262974	HRCEpiC	kidney:	n/a
45	chr7:5262924-5262974	NHDF-neo	bronchial:	n/a
46	chr7:5262924-5262974	U87	brain:	n/a
47	chr7:5262924-5262974	BJ	skin:	n/a
48	chr7:5262924-5262974	MCF10A-Er-Src	breast:	n/a
49	chr7:5262924-5262974	SKMC	muscle:	n/a
50	chr7:5262924-5262974	BE2_C	brain:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:5261238..5265959-chr7:5267428..5270937,4	K562	blood:
2	chr7:5261169..5263977-chr7:5465004..5466955,3	MCF-7	breast:
3	chr7:5261463..5263943-chr7:5264334..5266476,2	MCF-7	breast:
4	chr7:5261238..5263855-chr7:5267428..5269480,3	K562	blood:
5	chr7:5260514..5264813-chr7:5463021..5466900,4	MCF-7	breast:

No data

Variant related genes	Relation type
WIPI2	TF binding region
WIPI2	CpG island
ENSG00000182095	Chromatin interaction
ENSG00000272953	Chromatin interaction
ENSG00000157954	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10225429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10225919	1.00[AMR][1000 genomes]
rs10242373	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10243571	1.00[AMR][1000 genomes]
rs10245417	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10249285	1.00[AMR][1000 genomes]
rs10252983	1.00[AMR][1000 genomes]
rs10253380	1.00[AMR][1000 genomes]
rs10270945	1.00[AMR][1000 genomes]
rs10273014	1.00[AMR][1000 genomes]
rs10279924	1.00[AMR][1000 genomes]
rs28411908	1.00[AMR][1000 genomes]
rs28447119	1.00[AMR][1000 genomes]
rs28450156	1.00[AMR][1000 genomes]
rs28461705	1.00[AMR][1000 genomes]
rs6973436	1.00[AMR][1000 genomes]
rs6979367	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
5	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
6	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
7	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
8	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
9	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

No data

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	chr7:5249000-5269200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:5249000-5269200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr7:5249000-5269600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr7:5249000-5269800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:5249000-5271200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:5249000-5272600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:5249000-5272800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:5249000-5272800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:5249000-5273000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr7:5249000-5273200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr7:5249000-5273600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:5249000-5273600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:5249200-5269400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:5249200-5271800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:5249200-5272200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:5249200-5272400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:5249200-5272600	Strong transcription	Osteobl	bone
34	chr7:5249200-5272800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:5249200-5273000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr7:5249200-5273400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:5249200-5273400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:5249200-5273400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:5249200-5273400	Strong transcription	Fetal Stomach	stomach
40	chr7:5249200-5273400	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr7:5249200-5273600	Strong transcription	Fetal Intestine Small	intestine
42	chr7:5249400-5272400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr7:5249600-5272800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:5249600-5273400	Strong transcription	Right Ventricle	heart
45	chr7:5249800-5273600	Strong transcription	Fetal Brain Female	brain
46	chr7:5250000-5270000	Strong transcription	Brain Hippocampus Middle	brain
47	chr7:5250000-5270200	Strong transcription	Esophagus	oesophagus
48	chr7:5250200-5269000	Strong transcription	Spleen	Spleen
49	chr7:5250200-5272200	Strong transcription	Ovary	ovary
50	chr7:5250200-5272400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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