Variant report

Variant	rs28391588
Chromosome Location	chr15:58977856-58977857
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11071396	0.83[AMR][1000 genomes]
rs11852241	0.89[AMR][1000 genomes]
rs12437552	0.92[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2054096	0.91[JPT][hapmap];0.93[YRI][hapmap]
rs2414606	0.91[CEU][hapmap];0.83[CHB][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2414607	0.84[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes]
rs3933541	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs394845	0.96[GIH][hapmap];0.86[MEX][hapmap]
rs4238331	0.89[CHD][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs4774311	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs655348	0.87[AMR][1000 genomes]
rs681711	0.83[AMR][1000 genomes]
rs694335	0.93[GIH][hapmap];0.85[MEX][hapmap]
rs7163515	0.91[JPT][hapmap];0.86[YRI][hapmap]
rs7164844	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap]
rs7164954	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7168275	0.89[AMR][1000 genomes]
rs7170538	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs7171198	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7173286	0.92[CEU][hapmap];0.89[AMR][1000 genomes]
rs7176436	0.93[GIH][hapmap]
rs7179724	0.84[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7182060	0.93[GIH][hapmap]
rs7183504	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8023706	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes]
rs8027998	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9646204	0.80[MEX][hapmap]
rs9788674	0.85[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
2	chr15:58923400-58982800	Weak transcription	Lung	lung
3	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:58936200-58991400	Weak transcription	HMEC	breast
5	chr15:58951200-58987000	Weak transcription	NHEK	skin
6	chr15:58951600-58981800	Weak transcription	Fetal Brain Male	brain
7	chr15:58955200-58988400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:58956600-58984400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:58956600-58984600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:58956600-58987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:58956800-58980000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr15:58956800-58982000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:58957400-58984400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:58957600-58989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr15:58958800-58989000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:58960400-58982800	Weak transcription	Aorta	Aorta
17	chr15:58960400-58989600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:58961600-58987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:58961800-58984600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:58962000-58986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:58962000-58987200	Weak transcription	Fetal Lung	lung
22	chr15:58968200-58984000	Weak transcription	Brain Germinal Matrix	brain
23	chr15:58968400-58987000	Weak transcription	Fetal Kidney	kidney
24	chr15:58969200-58984200	Weak transcription	Fetal Intestine Large	intestine
25	chr15:58970600-58987200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:58971200-58982400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:58971400-58982000	Weak transcription	Primary T cells from cord blood	blood
28	chr15:58971400-58982800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr15:58971400-58982800	Weak transcription	Dnd41	blood
30	chr15:58971800-58982800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr15:58971800-58984800	Weak transcription	NHDF-Ad	bronchial
32	chr15:58971800-58986800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:58972000-58986600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:58972400-58982800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:58972400-58984200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:58972600-58983000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:58972600-58983000	Weak transcription	Spleen	Spleen
38	chr15:58972600-58984400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:58972600-58984400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:58972600-58988400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:58972600-58988800	Weak transcription	Fetal Stomach	stomach
42	chr15:58972600-58989000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:58973200-58978200	Weak transcription	Thymus	Thymus
44	chr15:58973200-58984600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr15:58973200-58984800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:58973600-58982400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:58973600-58984200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:58974600-58982400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:58974600-58991000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:58975200-58982200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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