Variant report

Variant	rs12983492
Chromosome Location	chr19:38742846-38742847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38741148..38742854-chr19:38800133..38802964,2	K562	blood:
2	chr19:38741131..38744022-chr19:38825237..38827049,2	K562	blood:
3	chr19:38738453..38743024-chr19:38754092..38756254,6	MCF-7	breast:
4	chr19:38741825..38743581-chr19:38794089..38796220,2	K562	blood:
5	chr19:38715033..38716998-chr19:38741502..38743244,2	K562	blood:
6	chr19:38721780..38723384-chr19:38741406..38743027,2	K562	blood:

Variant related genes	Relation type
ENSG00000167642	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000167644	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12609354	0.83[ASN][1000 genomes]
rs12610606	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs12610650	0.81[MEX][hapmap]
rs12610791	0.90[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs12975244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981507	0.86[ASN][1000 genomes]
rs2074982	0.81[MEX][hapmap]
rs2304177	1.00[ASW][hapmap]
rs35946591	0.87[ASN][1000 genomes]
rs4802323	1.00[ASW][hapmap]
rs4802327	1.00[ASW][hapmap]
rs6508781	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs6508782	0.81[ASN][1000 genomes]
rs71337551	0.92[EUR][1000 genomes]
rs7259936	0.85[CHB][hapmap];0.84[MEX][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12983492	CYP2B6	cis	parietal	SCAN
rs12983492	OPA3	cis	cerebellum	SCAN
rs12983492	ZNF233	cis	cerebellum	SCAN
rs12983492	C19orf61	cis	cerebellum	SCAN
rs12983492	RPS16	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38734800-38743800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr19:38738600-38743000	Enhancers	Fetal Intestine Large	intestine
3	chr19:38740400-38745800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr19:38741200-38743200	Enhancers	Stomach Mucosa	stomach
5	chr19:38741200-38743400	Enhancers	Pancreas	Pancrea
6	chr19:38741200-38744000	Enhancers	Duodenum Mucosa	Duodenum
7	chr19:38741200-38744400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:38741200-38744400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:38741200-38744600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:38741400-38743200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:38741400-38743200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:38741400-38744000	Enhancers	Fetal Heart	heart
13	chr19:38741400-38744400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:38741400-38744800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:38741400-38744800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:38741400-38744800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:38741400-38744800	Genic enhancers	A549	lung
18	chr19:38741400-38744800	Enhancers	HMEC	breast
19	chr19:38741600-38743000	Enhancers	Primary B cells from cord blood	blood
20	chr19:38741600-38743000	Weak transcription	Spleen	Spleen
21	chr19:38741600-38743200	Enhancers	Esophagus	oesophagus
22	chr19:38741600-38744200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:38741600-38744400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr19:38741600-38744600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr19:38741800-38743000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:38741800-38743000	Enhancers	Primary B cells from peripheral blood	blood
27	chr19:38741800-38743000	Active TSS	Stomach Smooth Muscle	stomach
28	chr19:38741800-38743000	Enhancers	HUVEC	blood vessel
29	chr19:38741800-38743200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:38741800-38743400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr19:38741800-38744200	Active TSS	Aorta	Aorta
32	chr19:38741800-38744200	Enhancers	Fetal Brain Male	brain
33	chr19:38741800-38744600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:38741800-38744600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr19:38741800-38744600	Enhancers	NHDF-Ad	bronchial
36	chr19:38741800-38744800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr19:38742000-38743000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:38742000-38743200	Enhancers	NH-A	brain
39	chr19:38742000-38743400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
40	chr19:38742000-38744000	Flanking Active TSS	Fetal Stomach	stomach
41	chr19:38742000-38744200	Active TSS	Left Ventricle	heart
42	chr19:38742000-38744400	Enhancers	Primary hematopoietic stem cells	blood
43	chr19:38742000-38744400	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr19:38742200-38743000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr19:38742200-38743000	Bivalent Enhancer	HepG2	liver
46	chr19:38742200-38743400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr19:38742200-38743600	Active TSS	Right Ventricle	heart
48	chr19:38742200-38744400	Active TSS	Right Atrium	heart
49	chr19:38742400-38743000	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr19:38742400-38743000	Enhancers	Colonic Mucosa	Colon

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