Variant report

Variant	rs28718778
Chromosome Location	chr15:41064934-41064935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41064920-41065074	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:41064630-41065178	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41064091..41066187-chr15:41067513..41070158,2	K562	blood:
2	chr15:41058708..41062204-chr15:41062731..41065541,5	K562	blood:
3	chr15:41062391..41066610-chr15:41066936..41069911,4	MCF-7	breast:
4	chr15:41024400..41027311-chr15:41063021..41065498,2	K562	blood:
5	chr15:41054628..41058503-chr15:41058814..41065530,15	K562	blood:

No data

Variant related genes	Relation type
DNAJC17	TF binding region
ENSG00000104129	Chromatin interaction
ENSG00000188277	Chromatin interaction
ENSG00000137880	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12102251	0.85[AMR][1000 genomes]
rs16970995	0.85[AMR][1000 genomes]
rs16970997	0.85[AMR][1000 genomes]
rs16971004	0.85[AMR][1000 genomes]
rs16971008	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16971013	1.00[AMR][1000 genomes]
rs16971015	1.00[AMR][1000 genomes]
rs1814415	0.85[AMR][1000 genomes]
rs2004043	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2412552	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28460049	0.85[AMR][1000 genomes]
rs28480346	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28498351	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28578011	0.85[AMR][1000 genomes]
rs28716513	0.83[AMR][1000 genomes]
rs28727420	0.85[AMR][1000 genomes]
rs28736321	0.85[AMR][1000 genomes]
rs34819163	0.83[AMR][1000 genomes]
rs4343248	0.85[AMR][1000 genomes]
rs57191378	0.85[AMR][1000 genomes]
rs57380807	0.85[AMR][1000 genomes]
rs58036350	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61317135	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61405952	0.85[AMR][1000 genomes]
rs6492966	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7165694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166719	0.85[AMR][1000 genomes]
rs7172251	0.83[AMR][1000 genomes]
rs7178363	0.85[AMR][1000 genomes]
rs7182456	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73398510	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73398512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73398517	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398522	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73398528	0.85[AMR][1000 genomes]
rs73398537	0.85[AMR][1000 genomes]
rs73398540	0.85[AMR][1000 genomes]
rs73398560	0.85[AMR][1000 genomes]
rs73398591	0.85[AMR][1000 genomes]
rs934783	0.83[AFR][1000 genomes];1.00[AMR][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	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv827306	chr15:41064643-41065465	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41057200-41065400	Weak transcription	Brain Angular Gyrus	brain
2	chr15:41057200-41068200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:41057400-41070800	Weak transcription	Psoas Muscle	Psoas
4	chr15:41057600-41066600	Weak transcription	Fetal Heart	heart
5	chr15:41057600-41067400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41058000-41069000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:41058200-41066800	Weak transcription	Fetal Kidney	kidney
8	chr15:41058200-41067400	Weak transcription	A549	lung
9	chr15:41058400-41068800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:41058600-41065600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:41058600-41072400	Strong transcription	Placenta	Placenta
12	chr15:41059000-41065400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:41059000-41065600	Weak transcription	NHDF-Ad	bronchial
14	chr15:41059200-41072400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:41059400-41066800	Weak transcription	K562	blood
16	chr15:41059600-41065400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:41059600-41066600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:41059600-41066600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:41059600-41069000	Strong transcription	NHLF	lung
20	chr15:41059800-41066200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:41059800-41072600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:41060000-41065400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:41060000-41072800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:41060400-41065400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:41060800-41065000	Genic enhancers	Liver	Liver
26	chr15:41061200-41065600	Weak transcription	Small Intestine	intestine
27	chr15:41061800-41065200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:41062200-41069400	Strong transcription	Aorta	Aorta
29	chr15:41062200-41072600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:41062200-41072600	Strong transcription	Fetal Brain Female	brain
31	chr15:41062200-41072600	Strong transcription	Right Ventricle	heart
32	chr15:41062200-41072600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr15:41062200-41072800	Strong transcription	Fetal Stomach	stomach
34	chr15:41062400-41066400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:41062400-41067000	Weak transcription	Fetal Brain Male	brain
36	chr15:41062400-41068800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:41062400-41068800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr15:41062400-41069800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:41062400-41072600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:41062400-41079400	Weak transcription	Right Atrium	heart
41	chr15:41062600-41065200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:41062600-41065200	Weak transcription	Brain Anterior Caudate	brain
43	chr15:41062600-41068600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:41062600-41068800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr15:41062600-41068800	Weak transcription	NH-A	brain
46	chr15:41062600-41072400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:41062600-41072600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr15:41062600-41072600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:41062600-41072600	Strong transcription	Brain Germinal Matrix	brain
50	chr15:41062600-41079000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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