Variant report

Variant	rs28638143
Chromosome Location	chr4:102133414-102133415
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:102131746..102133996-chr4:102142309..102145275,2	MCF-7	breast:
2	chr4:102132378..102137529-chr4:102267092..102270901,7	MCF-7	breast:
3	chr4:102129760..102133881-chr4:102266334..102270307,6	MCF-7	breast:
4	chr4:102119014..102119905-chr4:102132461..102133442,2	MCF-7	breast:
5	chr4:102116031..102123578-chr4:102130356..102136503,10	MCF-7	breast:
6	chr4:102132632..102134649-chr4:102137778..102139733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254531	Chromatin interaction
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10004830	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10019627	1.00[EUR][1000 genomes]
rs10027301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17030915	1.00[EUR][1000 genomes]
rs17030959	1.00[EUR][1000 genomes]
rs17030989	1.00[EUR][1000 genomes]
rs28379119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28421266	1.00[EUR][1000 genomes]
rs28464050	1.00[EUR][1000 genomes]
rs28491829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28534411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28542998	1.00[EUR][1000 genomes]
rs28553282	1.00[EUR][1000 genomes]
rs28614035	1.00[EUR][1000 genomes]
rs28640942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28675750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723066	1.00[EUR][1000 genomes]
rs58084948	1.00[EUR][1000 genomes]
rs58598913	1.00[EUR][1000 genomes]
rs58898502	1.00[EUR][1000 genomes]
rs6811228	1.00[EUR][1000 genomes]
rs72919782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998913	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102128000-102138200	Weak transcription	Primary B cells from cord blood	blood
2	chr4:102129000-102140400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr4:102129600-102135600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:102129600-102138600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:102131600-102133600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr4:102131800-102146000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:102132200-102133600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr4:102132200-102133600	Enhancers	Osteobl	bone
9	chr4:102132200-102133800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:102132200-102133800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:102132400-102133600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:102132400-102138400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:102132600-102133800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:102132800-102134000	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr4:102132800-102135000	Weak transcription	Stomach Mucosa	stomach
16	chr4:102133000-102135200	Weak transcription	Small Intestine	intestine
17	chr4:102133000-102135600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:102133000-102137800	Weak transcription	Ovary	ovary
19	chr4:102133000-102138200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:102133000-102138200	Weak transcription	NHDF-Ad	bronchial
21	chr4:102133000-102138400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:102133000-102138600	Weak transcription	NH-A	brain
23	chr4:102133000-102143800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:102133000-102143800	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:102133200-102134000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:102133200-102134600	Enhancers	A549	lung
27	chr4:102133200-102138600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:102133200-102142400	Weak transcription	HSMM	muscle
29	chr4:102133200-102143600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:102133400-102133600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr4:102133400-102133600	Enhancers	Right Atrium	heart
32	chr4:102133400-102133800	Enhancers	Psoas Muscle	Psoas
33	chr4:102133400-102139000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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