Variant report

Variant	rs863944
Chromosome Location	chr16:58766287-58766288
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	EBF1	chr16:58766099-58767314	GM12878	blood:	n/a	chr16:58766612-58766623 chr16:58766614-58766623

No.	Distal block	Cell Line	Cell type
1	chr16:58742292..58743873-chr16:58764921..58766535,2	K562	blood:
2	chr16:58521363..58523239-chr16:58765516..58767587,2	K562	blood:
3	chr16:58763681..58765319-chr16:58765617..58767662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245768	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1058192	0.81[EUR][1000 genomes]
rs11076262	0.89[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs12595974	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs12598527	0.89[CHB][hapmap]
rs12600201	0.89[CHB][hapmap];0.86[MEX][hapmap]
rs12600206	0.89[CHB][hapmap];0.86[MEX][hapmap]
rs14221	0.85[EUR][1000 genomes]
rs1595181	0.89[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap]
rs1615326	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap]
rs1646267	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646270	0.82[ASN][1000 genomes]
rs1657162	0.80[ASN][1000 genomes]
rs171786	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs173992	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs183757	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185397	0.89[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs187277	0.85[EUR][1000 genomes]
rs190473	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs257616	0.89[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs257617	0.85[EUR][1000 genomes]
rs257618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257619	0.85[EUR][1000 genomes]
rs257620	0.89[CEU][hapmap];0.93[TSI][hapmap]
rs257621	0.84[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs257630	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs257631	0.85[EUR][1000 genomes]
rs257632	0.85[EUR][1000 genomes]
rs257633	0.85[EUR][1000 genomes]
rs257634	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257636	0.80[EUR][1000 genomes]
rs257637	0.85[EUR][1000 genomes]
rs257638	0.81[EUR][1000 genomes]
rs30835	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs30839	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6993	0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

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	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
3	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
4	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs863944	CETP	cis	parietal	SCAN
rs863944	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs863944	GOT2	cis	Thyroid	GTEx
rs863944	GOT2	cis	cerebellum	SCAN
rs863944	MNDA	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58738400-58766600	Weak transcription	Stomach Mucosa	stomach
2	chr16:58747800-58767000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:58752600-58766600	Weak transcription	NHLF	lung
4	chr16:58753200-58766400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:58753200-58766600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr16:58753200-58766800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:58753400-58766400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr16:58754000-58766800	Weak transcription	Esophagus	oesophagus
9	chr16:58755200-58766800	Weak transcription	Fetal Lung	lung
10	chr16:58755400-58766800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:58755600-58766400	Weak transcription	Fetal Brain Male	brain
12	chr16:58756200-58766800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr16:58756200-58766800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr16:58756200-58766800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr16:58756400-58766400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr16:58757000-58766600	Weak transcription	Colonic Mucosa	Colon
17	chr16:58757000-58767400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr16:58757200-58766600	Weak transcription	Brain Germinal Matrix	brain
19	chr16:58757600-58766600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr16:58757600-58766600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr16:58757600-58767000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr16:58757800-58766600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:58757800-58766600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr16:58757800-58766600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr16:58757800-58766600	Weak transcription	Thymus	Thymus
26	chr16:58757800-58766600	Weak transcription	HSMM	muscle
27	chr16:58757800-58766800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr16:58757800-58766800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr16:58757800-58766800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr16:58757800-58766800	Weak transcription	Adipose Nuclei	Adipose
31	chr16:58757800-58766800	Weak transcription	Placenta	Placenta
32	chr16:58757800-58766800	Weak transcription	HSMMtube	muscle
33	chr16:58757800-58766800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr16:58757800-58767000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr16:58758000-58766400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr16:58758000-58766600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:58758000-58766800	Weak transcription	Aorta	Aorta
38	chr16:58758000-58766800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr16:58758000-58767000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr16:58758200-58766600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr16:58758400-58766800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr16:58758800-58766800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr16:58759000-58766400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr16:58759000-58766800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr16:58759000-58767200	Weak transcription	Lung	lung
46	chr16:58759800-58766600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr16:58761600-58766600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr16:58761600-58766800	Weak transcription	Gastric	stomach
49	chr16:58761600-58766800	Weak transcription	Right Ventricle	heart
50	chr16:58761800-58766600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links