Variant report

Variant	rs28412669
Chromosome Location	chr15:77176838-77176839
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:77176687-77176856	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SCAPER	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11072640	1.00[AMR][1000 genomes]
rs11853683	1.00[AMR][1000 genomes]
rs2469198	1.00[AMR][1000 genomes]
rs2469207	1.00[AMR][1000 genomes]
rs2469237	1.00[AMR][1000 genomes]
rs28391551	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28421596	1.00[AMR][1000 genomes]
rs28508056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28641730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28644501	1.00[AMR][1000 genomes]
rs28744566	1.00[AMR][1000 genomes]
rs3099135	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3099141	0.80[AFR][1000 genomes]
rs3110376	1.00[AMR][1000 genomes]
rs3110377	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3110383	1.00[AMR][1000 genomes]
rs3110386	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4886833	1.00[AMR][1000 genomes]
rs7173333	1.00[AMR][1000 genomes]
rs7178723	1.00[AMR][1000 genomes]
rs8026664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8035685	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8038253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8038701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920797	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
3	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv1803942	chr15:77151005-77210457	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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	18 gene(s)	inside rSNPs	diseases
9	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
5	chr15:77144800-77179000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:77146400-77196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:77147800-77177200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:77148600-77195600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:77148800-77181000	Weak transcription	Fetal Kidney	kidney
10	chr15:77148800-77195600	Weak transcription	Dnd41	blood
11	chr15:77154400-77179600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr15:77158600-77179800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:77158600-77180600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:77158600-77190800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:77158800-77177800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:77158800-77195600	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:77158800-77195600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:77161400-77188800	Weak transcription	Fetal Heart	heart
19	chr15:77166800-77177800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:77167600-77177200	Weak transcription	Hela-S3	cervix
21	chr15:77168000-77179600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:77168000-77179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:77168200-77177400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr15:77168400-77179400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:77168400-77195000	Weak transcription	Adipose Nuclei	Adipose
26	chr15:77168600-77177200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:77168600-77178000	Weak transcription	Gastric	stomach
28	chr15:77168600-77179600	Weak transcription	Lung	lung
29	chr15:77168600-77180000	Weak transcription	Esophagus	oesophagus
30	chr15:77168600-77180800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:77168600-77181600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:77168600-77195000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:77168600-77195600	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:77168600-77196800	Weak transcription	Pancreas	Pancrea
35	chr15:77168600-77196800	Weak transcription	Spleen	Spleen
36	chr15:77168800-77179200	Weak transcription	Fetal Brain Female	brain
37	chr15:77169400-77179200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:77170200-77190600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:77172000-77179200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:77172200-77182400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:77172800-77195600	Weak transcription	HSMM	muscle
42	chr15:77173400-77178400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:77173400-77179200	Weak transcription	HepG2	liver
44	chr15:77173600-77179800	Weak transcription	Brain Substantia Nigra	brain
45	chr15:77173800-77183600	Weak transcription	Primary T cells from cord blood	blood
46	chr15:77174200-77179600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:77174800-77179000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:77175400-77179200	Weak transcription	Fetal Intestine Small	intestine
49	chr15:77175400-77179200	Weak transcription	Thymus	Thymus
50	chr15:77175600-77177200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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