Variant report

Variant	rs28539201
Chromosome Location	chr15:43427012-43427013
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43426566..43429300-chr15:43440939..43443897,2	K562	blood:
2	chr15:43412581..43417001-chr15:43422670..43429913,10	K562	blood:
3	chr15:43395932..43399418-chr15:43425897..43428585,4	K562	blood:
4	chr15:43396979..43399675-chr15:43425245..43427228,2	MCF-7	breast:
5	chr15:43424880..43427064-chr15:51913097..51915072,2	MCF-7	breast:
6	chr15:43424687..43428034-chr15:43433131..43438698,7	K562	blood:

Variant related genes	Relation type
ENSG00000159459	Chromatin interaction
ENSG00000104093	Chromatin interaction
ENSG00000137842	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10048057	1.00[EUR][1000 genomes]
rs10083725	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10152237	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10220812	1.00[EUR][1000 genomes]
rs1042168	1.00[EUR][1000 genomes]
rs10438267	1.00[EUR][1000 genomes]
rs1078243	1.00[EUR][1000 genomes]
rs11504654	1.00[EUR][1000 genomes]
rs11504655	1.00[EUR][1000 genomes]
rs12324094	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12324436	1.00[EUR][1000 genomes]
rs12324573	1.00[EUR][1000 genomes]
rs1474199	1.00[EUR][1000 genomes]
rs1520519	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16957409	1.00[EUR][1000 genomes]
rs16957462	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16957499	1.00[EUR][1000 genomes]
rs16957502	1.00[EUR][1000 genomes]
rs16957507	1.00[EUR][1000 genomes]
rs1863601	1.00[EUR][1000 genomes]
rs2271964	1.00[EUR][1000 genomes]
rs2271965	1.00[EUR][1000 genomes]
rs28444219	1.00[EUR][1000 genomes]
rs3177296	1.00[EUR][1000 genomes]
rs34222269	1.00[EUR][1000 genomes]
rs4419035	1.00[EUR][1000 genomes]
rs505276	1.00[EUR][1000 genomes]
rs58059509	1.00[EUR][1000 genomes]
rs59401274	1.00[EUR][1000 genomes]
rs59900401	1.00[EUR][1000 genomes]
rs60435696	1.00[EUR][1000 genomes]
rs60481556	1.00[EUR][1000 genomes]
rs61268760	1.00[EUR][1000 genomes]
rs61343376	1.00[EUR][1000 genomes]
rs61711558	1.00[EUR][1000 genomes]
rs7162620	1.00[EUR][1000 genomes]
rs7162971	1.00[EUR][1000 genomes]
rs7171797	1.00[EUR][1000 genomes]
rs7176183	1.00[EUR][1000 genomes]
rs7182685	1.00[EUR][1000 genomes]
rs7183024	1.00[EUR][1000 genomes]
rs8030850	1.00[EUR][1000 genomes]
rs8035881	1.00[EUR][1000 genomes]
rs8039342	1.00[EUR][1000 genomes]
rs8040769	1.00[EUR][1000 genomes]
rs8040960	1.00[EUR][1000 genomes]
rs8041312	1.00[EUR][1000 genomes]
rs9806236	1.00[EUR][1000 genomes]
rs9806629	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9972314	1.00[EUR][1000 genomes]
rs9972367	1.00[EUR][1000 genomes]
rs999025	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43425000-43427200	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr15:43425000-43427200	Active TSS	Fetal Intestine Large	intestine
3	chr15:43425400-43427200	Active TSS	Duodenum Mucosa	Duodenum
4	chr15:43426200-43427200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:43426200-43427200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr15:43426200-43427200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:43426200-43427200	Flanking Active TSS	Hela-S3	cervix
8	chr15:43426200-43427200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr15:43426400-43427200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:43426400-43427200	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr15:43426600-43427200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:43426600-43427200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:43426600-43427600	Enhancers	Stomach Mucosa	stomach
14	chr15:43426600-43428800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:43426600-43429600	Weak transcription	Gastric	stomach
16	chr15:43426600-43442200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:43426800-43427200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr15:43426800-43427200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr15:43426800-43427200	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr15:43426800-43427200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr15:43426800-43427200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:43426800-43427200	Enhancers	Liver	Liver
23	chr15:43426800-43427200	Enhancers	Small Intestine	intestine
24	chr15:43426800-43427200	Flanking Active TSS	HepG2	liver
25	chr15:43426800-43427400	Enhancers	Primary B cells from cord blood	blood
26	chr15:43426800-43427400	Enhancers	Primary B cells from peripheral blood	blood
27	chr15:43426800-43427400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:43426800-43427400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr15:43426800-43427400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr15:43426800-43427400	Enhancers	Brain Cingulate Gyrus	brain
31	chr15:43426800-43427400	Flanking Active TSS	GM12878-XiMat	blood
32	chr15:43426800-43427400	Flanking Active TSS	NHDF-Ad	bronchial
33	chr15:43426800-43427600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:43426800-43427800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:43426800-43427800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:43426800-43427800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
37	chr15:43426800-43427800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:43426800-43427800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:43426800-43427800	Enhancers	Fetal Kidney	kidney
40	chr15:43426800-43428600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:43426800-43428600	Weak transcription	Ovary	ovary
42	chr15:43426800-43428800	Weak transcription	Colonic Mucosa	Colon
43	chr15:43426800-43428800	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:43426800-43428800	Weak transcription	Placenta	Placenta
45	chr15:43426800-43428800	Weak transcription	Left Ventricle	heart
46	chr15:43426800-43428800	Weak transcription	Lung	lung
47	chr15:43426800-43428800	Weak transcription	Pancreas	Pancrea
48	chr15:43426800-43429000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:43426800-43429000	Weak transcription	Aorta	Aorta
50	chr15:43426800-43429000	Weak transcription	Fetal Muscle Trunk	muscle

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