Variant report

Variant	rs28650493
Chromosome Location	chr4:87814876-87814877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:87814817-87814961	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:87814791-87815000	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87515391..87517685-chr4:87812251..87815383,4	MCF-7	breast:

Variant related genes	Relation type
C4orf36	TF binding region
ENSG00000163629	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10011798	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10015121	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10015477	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021020	0.94[ASN][1000 genomes]
rs10021790	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10034336	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1010902	0.97[ASN][1000 genomes]
rs1010903	0.97[ASN][1000 genomes]
rs13115795	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120981	0.94[ASN][1000 genomes]
rs13137483	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17012132	0.86[ASN][1000 genomes]
rs1985944	0.97[ASN][1000 genomes]
rs2121871	0.94[ASN][1000 genomes]
rs28446826	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs28641910	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716151	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35428486	0.93[ASN][1000 genomes]
rs55698195	0.88[ASN][1000 genomes]
rs56201068	0.92[ASN][1000 genomes]
rs6823051	0.97[ASN][1000 genomes]
rs6846822	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72667703	0.97[ASN][1000 genomes]
rs72667705	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87814000-87815000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr4:87814000-87815600	Weak transcription	Hela-S3	cervix
3	chr4:87814000-87817400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:87814000-87825000	Weak transcription	Right Atrium	heart
5	chr4:87814000-87825200	Weak transcription	Left Ventricle	heart
6	chr4:87814200-87815400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:87814200-87815600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:87814200-87817200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:87814200-87824800	Weak transcription	Adipose Nuclei	Adipose
10	chr4:87814200-87825000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:87814200-87825200	Weak transcription	Right Ventricle	heart
12	chr4:87814200-87825200	Weak transcription	A549	lung
13	chr4:87814200-87829400	Weak transcription	K562	blood
14	chr4:87814400-87815400	Weak transcription	HUVEC	blood vessel
15	chr4:87814400-87815400	Weak transcription	NH-A	brain
16	chr4:87814400-87815600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:87814400-87815600	Weak transcription	HMEC	breast
18	chr4:87814400-87815600	Weak transcription	NHDF-Ad	bronchial
19	chr4:87814400-87815600	Weak transcription	Osteobl	bone
20	chr4:87814400-87816000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:87814400-87825000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:87814400-87825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:87814400-87825200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:87814600-87815000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:87814600-87815600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:87814600-87815600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:87814600-87815600	Weak transcription	NHLF	lung
28	chr4:87814600-87815800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:87814600-87816000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:87814600-87821600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:87814600-87821600	Weak transcription	Placenta	Placenta
32	chr4:87814600-87825200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:87814600-87830000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:87814800-87815800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:87814800-87818000	Enhancers	NHEK	skin

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