Variant report

Variant	rs28514561
Chromosome Location	chr19:42947097-42947098
allele	A/C
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	E2F6	chr19:42946928-42947485	H1-hESC	embryonic stem cell:	n/a	chr19:42947300-42947307 chr19:42947300-42947307 chr19:42947299-42947311 chr19:42947300-42947307
2	MYC	chr19:42947041-42947339	MCF10A-Er-Src	breast:	n/a	chr19:42947063-42947072
3	FOS	chr19:42946902-42947446	MCF10A-Er-Src	breast:	n/a	chr19:42947063-42947070 chr19:42947063-42947071 chr19:42947062-42947072 chr19:42947063-42947071
4	CEBPB	chr19:42947076-42947234	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr19:42947028-42947326	MCF10A-Er-Src	breast:	n/a	chr19:42947190-42947198 chr19:42947188-42947199
6	CEBPB	chr19:42947040-42947296	K562	blood:	n/a	n/a
7	STAT3	chr19:42947017-42947450	MCF10A-Er-Src	breast:	n/a	chr19:42947190-42947198 chr19:42947188-42947199
8	CEBPB	chr19:42946939-42947381	MCF-7	breast:	n/a	n/a
9	MYC	chr19:42946978-42947391	MCF10A-Er-Src	breast:	n/a	chr19:42947063-42947072
10	STAT3	chr19:42947017-42947427	MCF10A-Er-Src	breast:	n/a	chr19:42947190-42947198 chr19:42947188-42947199
11	MAX	chr19:42947087-42947455	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOS	chr19:42946997-42947325	MCF10A-Er-Src	breast:	n/a	chr19:42947063-42947070 chr19:42947063-42947071 chr19:42947062-42947072 chr19:42947063-42947071
13	FOS	chr19:42946970-42947370	MCF10A-Er-Src	breast:	n/a	chr19:42947063-42947070 chr19:42947063-42947071 chr19:42947062-42947072 chr19:42947063-42947071
14	CEBPB	chr19:42946985-42947328	HepG2	liver:	n/a	n/a
15	MAX	chr19:42946983-42947505	MCF-7	breast:	n/a	chr19:42947063-42947072
16	CEBPB	chr19:42947020-42947295	IMR90	lung:	n/a	n/a
17	STAT3	chr19:42946921-42947488	MCF10A-Er-Src	breast:	n/a	chr19:42947190-42947198 chr19:42947188-42947199
18	CEBPB	chr19:42947055-42947307	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOS	chr19:42947042-42947382	MCF10A-Er-Src	breast:	n/a	chr19:42947063-42947070 chr19:42947063-42947071 chr19:42947062-42947072 chr19:42947063-42947071
20	CEBPB	chr19:42947020-42947306	A549	lung:	n/a	n/a

Variant related genes	Relation type
CXCL17	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10405891	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411253	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414969	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416062	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416915	0.92[AMR][1000 genomes]
rs10417560	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422000	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423047	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423136	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10425139	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13345659	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975743	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975750	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17340417	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28448880	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35623577	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248439	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7251638	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252470	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7254369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7254839	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7255015	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73556352	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73556356	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8102976	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8103108	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42938000-42950200	Weak transcription	Gastric	stomach
2	chr19:42938000-42954200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:42943200-42947400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:42944600-42947200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr19:42944600-42947400	Enhancers	Primary B cells from cord blood	blood
6	chr19:42944600-42947600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr19:42944800-42947200	Enhancers	Fetal Thymus	thymus
8	chr19:42945200-42947200	Active TSS	Fetal Stomach	stomach
9	chr19:42945200-42948200	Weak transcription	Small Intestine	intestine
10	chr19:42945400-42947400	Enhancers	Primary T cells from cord blood	blood
11	chr19:42945400-42948000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:42945400-42948200	Weak transcription	Colonic Mucosa	Colon
13	chr19:42945600-42948000	Enhancers	HepG2	liver
14	chr19:42945600-42948200	Weak transcription	Spleen	Spleen
15	chr19:42945800-42947400	Active TSS	Stomach Mucosa	stomach
16	chr19:42945800-42948200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr19:42945800-42950200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:42946000-42947200	Active TSS	Esophagus	oesophagus
19	chr19:42946000-42948200	Weak transcription	Fetal Lung	lung
20	chr19:42946200-42953600	Weak transcription	Adipose Nuclei	Adipose
21	chr19:42946400-42949000	Enhancers	Fetal Intestine Large	intestine
22	chr19:42946600-42947200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:42946600-42947200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr19:42946600-42947600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr19:42946800-42947200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr19:42946800-42947200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr19:42946800-42947200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr19:42946800-42947200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr19:42946800-42947200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:42946800-42947200	Enhancers	Pancreas	Pancrea
31	chr19:42946800-42947600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr19:42946800-42948600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:42946800-42949000	Enhancers	Fetal Intestine Small	intestine
34	chr19:42946800-42949000	Enhancers	A549	lung
35	chr19:42946800-42949200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:42947000-42947200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr19:42947000-42947200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:42947000-42947200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:42947000-42947200	Enhancers	Lung	lung
40	chr19:42947000-42948200	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr19:42947000-42948600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr19:42947000-42949000	Enhancers	Liver	Liver
43	chr19:42947000-42952800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:42947000-42952800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:42947000-42952800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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