Variant report

Variant	rs5005127
Chromosome Location	chr4:48045003-48045004
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	chr4:48018543..48020121-chr4:48043793..48046506,2	MCF-7	breast:
2	chr4:48043679..48046228-chr4:48047228..48049577,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163293	Chromatin interaction
ENSG00000198515	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10517203	1.00[AMR][1000 genomes]
rs10517205	1.00[AMR][1000 genomes]
rs1396048	1.00[AMR][1000 genomes]
rs16860890	1.00[AMR][1000 genomes]
rs16860894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860898	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1911668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099742	1.00[AMR][1000 genomes]
rs4694881	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4694882	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6827424	1.00[AMR][1000 genomes]
rs6848406	1.00[AMR][1000 genomes]
rs73149663	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7690816	0.97[AFR][1000 genomes];1.00[AMR][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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
2	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
3	chr4:48026800-48045400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
5	chr4:48036400-48046400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:48038000-48047800	Weak transcription	NHEK	skin
7	chr4:48038200-48045200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:48038600-48045200	Weak transcription	Fetal Heart	heart
9	chr4:48038600-48053000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:48039000-48045400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:48041600-48053000	Weak transcription	HMEC	breast
12	chr4:48043000-48045200	Weak transcription	Stomach Mucosa	stomach
13	chr4:48043800-48045800	Flanking Active TSS	GM12878-XiMat	blood
14	chr4:48044200-48045600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:48044200-48045800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:48044200-48045800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr4:48044400-48045200	Enhancers	Duodenum Mucosa	Duodenum
18	chr4:48044400-48045800	Enhancers	Fetal Intestine Large	intestine
19	chr4:48044400-48046600	Enhancers	Primary B cells from peripheral blood	blood
20	chr4:48044600-48045200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr4:48044600-48045400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr4:48044600-48046000	Enhancers	Fetal Intestine Small	intestine
23	chr4:48044600-48049200	Enhancers	Primary B cells from cord blood	blood
24	chr4:48044800-48045200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:48044800-48045200	Enhancers	A549	lung
26	chr4:48044800-48045400	Enhancers	Fetal Kidney	kidney
27	chr4:48044800-48045600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:48044800-48045600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr4:48044800-48045600	Flanking Active TSS	Liver	Liver
30	chr4:48044800-48045600	Flanking Active TSS	HepG2	liver
31	chr4:48044800-48046000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:48044800-48049200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr4:48044800-48049400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:48045000-48045400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr4:48045000-48045600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr4:48045000-48045600	Enhancers	Primary hematopoietic stem cells	blood
37	chr4:48045000-48045600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr4:48045000-48045800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr4:48045000-48047200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:48045000-48049200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:48045000-48049400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:48045000-48049400	Enhancers	Primary T helper cells fromperipheralblood	blood

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