Variant report

Variant	rs28413601
Chromosome Location	chr4:22507237-22507238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22505951..22512123-chr4:22514706..22518696,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152990	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10016470	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516410	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10938904	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665589	1.00[ASN][1000 genomes]
rs4391016	1.00[ASN][1000 genomes]
rs6448161	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830414	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838873	1.00[ASN][1000 genomes]
rs7664547	1.00[ASN][1000 genomes]
rs9990711	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22488600-22516000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:22490200-22508600	Weak transcription	Right Atrium	heart
3	chr4:22497000-22515600	Weak transcription	Fetal Stomach	stomach
4	chr4:22500000-22508200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:22500400-22510600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr4:22500400-22510600	Enhancers	HMEC	breast
7	chr4:22500600-22507800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr4:22500600-22510800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:22500800-22507600	Weak transcription	Ovary	ovary
10	chr4:22501800-22508000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:22502200-22515600	Weak transcription	Primary T cells from cord blood	blood
12	chr4:22502800-22507800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:22502800-22509800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:22502800-22515600	Weak transcription	Fetal Kidney	kidney
15	chr4:22503000-22507600	Weak transcription	Stomach Mucosa	stomach
16	chr4:22503200-22508400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:22503200-22515600	Weak transcription	NHDF-Ad	bronchial
18	chr4:22503400-22508200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:22503400-22508200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr4:22504000-22508600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:22504000-22514200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:22504200-22507400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:22504800-22509200	Weak transcription	Placenta	Placenta
24	chr4:22504800-22509400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:22504800-22510800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:22504800-22512200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:22504800-22513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:22504800-22514200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:22505000-22509200	Weak transcription	NH-A	brain
30	chr4:22505000-22515200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:22505200-22509000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:22505200-22512200	Weak transcription	Fetal Intestine Large	intestine
33	chr4:22505400-22507400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:22505400-22507600	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:22505400-22507800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:22505400-22508200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr4:22505400-22509000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:22505400-22509000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:22505400-22509000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:22505400-22509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:22505400-22509800	Weak transcription	Hela-S3	cervix
42	chr4:22505400-22511800	Weak transcription	Fetal Intestine Small	intestine
43	chr4:22505400-22515400	Weak transcription	A549	lung
44	chr4:22505600-22507400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr4:22505600-22507400	Weak transcription	Small Intestine	intestine
46	chr4:22505600-22507800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:22505600-22509200	Weak transcription	Brain Anterior Caudate	brain
48	chr4:22505600-22510400	Enhancers	Liver	Liver
49	chr4:22505600-22513200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:22505600-22515600	Weak transcription	Rectal Mucosa Donor 29	rectum

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