Variant report

Variant	rs1021469
Chromosome Location	chr12:58208164-58208165
allele	C/T
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	MAFK	chr12:58208042-58208373	HepG2	liver:	n/a	n/a
2	RCOR1	chr12:58208027-58208546	HepG2	liver:	n/a	n/a
3	HEY1	chr12:58208029-58208418	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:58207564-58208745	SK-N-MC	brain:	n/a	n/a
5	MAZ	chr12:58208104-58208242	HepG2	liver:	n/a	chr12:58208202-58208211
6	POLR2A	chr12:58208000-58208600	HepG2	liver:	n/a	n/a
7	MYBL2	chr12:58207925-58208508	HepG2	liver:	n/a	n/a
8	SMC3	chr12:58208040-58208314	HepG2	liver:	n/a	n/a
9	HNF4A	chr12:58207984-58208401	HepG2	liver:	n/a	chr12:58208219-58208232 chr12:58208218-58208231 chr12:58208219-58208232 chr12:58208217-58208232
10	BRCA1	chr12:58208121-58208366	HepG2	liver:	n/a	n/a
11	CEBPB	chr12:58208014-58208408	HepG2	liver:	n/a	chr12:58208199-58208210
12	JUN	chr12:58208045-58208295	HepG2	liver:	n/a	chr12:58208200-58208213
13	NFIC	chr12:58208037-58208326	HepG2	liver:	n/a	n/a
14	CHD2	chr12:58208038-58208461	HepG2	liver:	n/a	n/a
15	RAD21	chr12:58208121-58208574	HepG2	liver:	n/a	n/a
16	JUND	chr12:58208096-58208360	HepG2	liver:	n/a	n/a
17	CEBPB	chr12:58208038-58208326	HepG2	liver:	n/a	chr12:58208199-58208210
18	NFIC	chr12:58208010-58208388	HepG2	liver:	n/a	n/a
19	POLR2A	chr12:58208094-58208622	U87	brain:	n/a	n/a
20	MBD4	chr12:58207978-58208346	HepG2	liver:	n/a	n/a
21	MYBL2	chr12:58207906-58208492	HepG2	liver:	n/a	n/a
22	HNF4G	chr12:58208018-58208445	HepG2	liver:	n/a	chr12:58208219-58208232 chr12:58208218-58208231 chr12:58208218-58208233 chr12:58208219-58208232
23	POLR2A	chr12:58207867-58208630	HepG2	liver:	n/a	n/a
24	HNF4A	chr12:58208010-58208360	HepG2	liver:	n/a	chr12:58208219-58208232 chr12:58208218-58208231 chr12:58208219-58208232 chr12:58208217-58208232
25	HNF4A	chr12:58207981-58208394	HepG2	liver:	n/a	chr12:58208219-58208232 chr12:58208218-58208231 chr12:58208219-58208232 chr12:58208217-58208232
26	POLR2A	chr12:58208092-58208433	HepG2	liver:	n/a	n/a
27	CEBPB	chr12:58208010-58208441	HepG2	liver:	n/a	chr12:58208199-58208210
28	TBP	chr12:58208106-58208331	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:58208107-58208549	SK-N-SH	brain:	n/a	n/a
30	ZNF263	chr12:58207686-58208188	HEK293-T-REx	kidney:	n/a	chr12:58207917-58207926
31	POLR2A	chr12:58208111-58208176	ProgFib	skin:	n/a	n/a
32	POLR2A	chr12:58207923-58208723	HepG2	liver:	n/a	n/a
33	EP300	chr12:58208007-58208349	HepG2	liver:	n/a	n/a
34	POLR2A	chr12:58206945-58208669	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58205281..58208353-chr12:58208928..58211653,3	MCF-7	breast:
2	chr12:58206978..58209497-chr12:58211355..58214120,3	K562	blood:
3	chr12:58205717..58208444-chr12:58209077..58210995,4	K562	blood:
4	chr12:58195714..58198546-chr12:58205658..58208467,2	K562	blood:
5	chr12:58137583..58140333-chr12:58207188..58209651,2	K562	blood:

Variant related genes	Relation type
ENSG00000269903	TF binding region
AVIL	TF binding region
ENSG00000135452	Chromatin interaction
ENSG00000270039	Chromatin interaction
ENSG00000135407	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 39 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10431505	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10431552	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10747783	0.91[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10783847	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783848	0.91[CEU][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877012	0.92[CEU][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877013	0.88[CEU][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.88[EUR][1000 genomes]
rs10877014	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877015	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877016	0.92[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877017	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877018	0.87[EUR][1000 genomes]
rs10877019	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172333	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172335	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172342	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172343	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172344	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172349	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172350	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172351	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1599931	0.82[JPT][hapmap]
rs1599932	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1875124	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1875125	0.83[JPT][hapmap]
rs2014886	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2069502	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs2069506	0.82[EUR][1000 genomes]
rs2072052	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.85[EUR][1000 genomes]
rs2291617	0.92[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782130	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3825079	0.92[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4646536	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760332	0.83[JPT][hapmap]
rs56177740	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581155	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs703842	0.92[CEU][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs724834	0.92[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7965287	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8181644	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs870392	0.83[JPT][hapmap]
rs871871	0.83[JPT][hapmap]
rs923829	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9652011	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:39)

SNP	Gene	Cis/trans	Tissue	Source
rs1021469	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs1021469	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs1021469	ESPL1	cis	parietal	SCAN
rs1021469	FAM119B	cis	Lymphoblastoid	GTEx
rs1021469	TSFM	cis	lymphoblastoid	seeQTL
rs1021469	FAM119B	cis	Cerebellum	GTEx
rs1021469	HSD17B6	cis	cerebellum	SCAN
rs1021469	TSFM	cis	thalamus	BrainEAC
rs1021469	CYP27B1	cis	Thyroid	GTEx
rs1021469	FAM119B	cis	cerebellum	SCAN
rs1021469	TSPAN31	cis	parietal	SCAN
rs1021469	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1021469	METTL21B	cis	Adipose Subcutaneous	GTEx
rs1021469	TSFM	cis	occipital cortex	BrainEAC
rs1021469	DKFZP586D0919	cis	multi-tissue	Pritchard
rs1021469	KIAA0748	cis	cerebellum	SCAN
rs1021469	TSFM	cis	cerebellum	SCAN
rs1021469	FAM119B	cis	Frontal Cortex	GTEx
rs1021469	FAM119B	cis	parietal	SCAN
rs1021469	METTL21B	cis	Esophagus Mucosa	GTEx
rs1021469	TSFM	cis	brain	BrainEAC
rs1021469	METTL21B	cis	Nerve Tibial	GTEx
rs1021469	TSFM	cis	multi-tissue	Pritchard
rs1021469	TSFM	cis	parietal	SCAN
rs1021469	METTL21B	cis	Esophagus Muscularis	GTEx
rs1021469	METTL21B	cis	Muscle Skeletal	GTEx
rs1021469	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs1021469	WIBG	cis	cerebellum	SCAN
rs1021469	CDK4	cis	cerebellum	SCAN
rs1021469	TSFM	cis	intralobular white matter	BrainEAC
rs1021469	TSPAN31	cis	cerebellum	SCAN
rs1021469	GPR84	cis	cerebellum	SCAN
rs1021469	KRT5	cis	cerebellum	SCAN
rs1021469	CDK2	cis	parietal	SCAN
rs1021469	TSFM	cis	cerebellar cortex	BrainEAC
rs1021469	XRCC6BP1	cis	multi-tissue	Pritchard
rs1021469	METTL21B	cis	Whole Blood	GTEx
rs1021469	TSFM	cis	temporal cortex	BrainEAC
rs1021469	FAM119B	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58181400-58216000	Weak transcription	Fetal Brain Male	brain
3	chr12:58187000-58216600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:58187200-58215600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:58189000-58208400	Strong transcription	Fetal Stomach	stomach
6	chr12:58189800-58208400	Strong transcription	Placenta	Placenta
7	chr12:58190200-58216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:58190800-58215200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:58190800-58216200	Weak transcription	HUVEC	blood vessel
10	chr12:58191000-58216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:58191200-58213600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:58191200-58216200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:58191800-58208400	Weak transcription	Psoas Muscle	Psoas
14	chr12:58192000-58210600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:58192200-58216200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:58193000-58210200	Strong transcription	Fetal Intestine Small	intestine
17	chr12:58193200-58215000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:58193400-58216200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:58194200-58215200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:58195200-58210600	Weak transcription	Small Intestine	intestine
21	chr12:58197200-58211600	Weak transcription	A549	lung
22	chr12:58197200-58216400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr12:58198400-58215000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:58200800-58212600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:58201200-58215000	Weak transcription	Fetal Kidney	kidney
26	chr12:58202400-58214800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:58202400-58215000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr12:58202400-58215200	Weak transcription	GM12878-XiMat	blood
29	chr12:58202600-58208200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:58202600-58214400	Weak transcription	Dnd41	blood
31	chr12:58203200-58211600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:58203200-58213600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:58203400-58216600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:58203600-58208200	Weak transcription	Fetal Lung	lung
35	chr12:58203800-58209200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:58203800-58210800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:58203800-58212000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:58203800-58214400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:58204000-58209200	Weak transcription	Fetal Thymus	thymus
40	chr12:58204200-58214000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:58204200-58216400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr12:58204600-58214800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:58204800-58209800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr12:58204800-58210600	Weak transcription	NHDF-Ad	bronchial
45	chr12:58204800-58212400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:58204800-58216200	Weak transcription	NHEK	skin
47	chr12:58205000-58209600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:58205000-58210600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:58205000-58212200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:58205000-58213200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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