Variant report

Variant	rs28568441
Chromosome Location	chr4:99388616-99388617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99388436..99389361-chr4:99666672..99667178,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10017792	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10030765	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10516431	0.81[AMR][1000 genomes]
rs12501972	0.97[ASN][1000 genomes]
rs12503056	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12508322	0.88[ASN][1000 genomes]
rs17027603	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913488	0.97[ASN][1000 genomes]
rs2090118	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28416087	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28733733	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28798461	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834829	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6835676	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845766	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73832309	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7664210	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7673119	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7675605	0.94[ASN][1000 genomes]
rs7676285	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99387800-99388800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:99388000-99388800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:99388000-99388800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:99388000-99388800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:99388000-99388800	Enhancers	HMEC	breast
6	chr4:99388000-99388800	Enhancers	NH-A	brain
7	chr4:99388000-99388800	Enhancers	NHEK	skin
8	chr4:99388000-99388800	Enhancers	Osteobl	bone
9	chr4:99388000-99390200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:99388200-99388800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:99388200-99388800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:99388200-99388800	Enhancers	Brain Substantia Nigra	brain
13	chr4:99388200-99388800	Enhancers	HSMMtube	muscle
14	chr4:99388400-99388800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr4:99388400-99388800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:99388400-99388800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:99388400-99388800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr4:99388400-99388800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:99388400-99388800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr4:99388400-99388800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr4:99388400-99388800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr4:99388400-99388800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:99388400-99388800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:99388400-99388800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:99388400-99388800	Enhancers	Brain Anterior Caudate	brain
26	chr4:99388400-99388800	Enhancers	Brain Germinal Matrix	brain
27	chr4:99388400-99388800	Enhancers	Brain Hippocampus Middle	brain
28	chr4:99388400-99388800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr4:99388400-99388800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:99388400-99388800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr4:99388400-99388800	Enhancers	Fetal Brain Male	brain
32	chr4:99388400-99388800	Enhancers	Fetal Muscle Leg	muscle
33	chr4:99388400-99388800	Enhancers	Fetal Thymus	thymus
34	chr4:99388400-99388800	Enhancers	Left Ventricle	heart
35	chr4:99388400-99388800	Enhancers	Ovary	ovary
36	chr4:99388400-99388800	Enhancers	Rectal Smooth Muscle	rectum
37	chr4:99388400-99388800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:99388400-99388800	Enhancers	NHLF	lung
39	chr4:99388400-99389400	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr4:99388400-99389400	Enhancers	Esophagus	oesophagus
41	chr4:99388400-99389600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:99388600-99388800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr4:99388600-99388800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr4:99388600-99388800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr4:99388600-99388800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr4:99388600-99388800	Enhancers	Primary hematopoietic stem cells	blood
47	chr4:99388600-99388800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:99388600-99388800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr4:99388600-99388800	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr4:99388600-99388800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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