Variant report

Variant	rs12490565
Chromosome Location	chr3:121553719-121553720
allele	A/G
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	MAX	chr3:121553413-121554408	H1-hESC	embryonic stem cell:	n/a	chr3:121554359-121554369
2	TAF1	chr3:121553424-121554480	H1-hESC	embryonic stem cell:	n/a	n/a
3	CREB1	chr3:121553643-121554243	A549	lung:	n/a	n/a
4	POLR2A	chr3:121553407-121554331	K562	blood:	n/a	n/a
5	POLR2A	chr3:121553539-121554456	GM12878	blood:	n/a	n/a
6	MTA3	chr3:121553158-121554784	GM12878	blood:	n/a	n/a
7	ELF1	chr3:121553661-121554107	K562	blood:	n/a	n/a
8	POLR2A	chr3:121553592-121554220	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF143	chr3:121553557-121554234	Hela-S3	cervix:	n/a	n/a
10	NFATC1	chr3:121553301-121553818	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:121553507-121554628	GM12878	blood:	n/a	n/a
12	ELF1	chr3:121553515-121554207	MCF-7	breast:	n/a	n/a
13	POLR2A	chr3:121553409-121554647	HL-60	blood:	n/a	n/a
14	MAX	chr3:121553455-121554635	HCT-116	colon:	n/a	chr3:121554359-121554369
15	SP4	chr3:121553582-121554072	H1-hESC	embryonic stem cell:	n/a	chr3:121553947-121553958
16	POLR2A	chr3:121553588-121554325	H1-neurons	neurons:	n/a	n/a
17	CREB1	chr3:121553694-121554170	K562	blood:	n/a	n/a
18	MAX	chr3:121553489-121554288	MCF-7	breast:	n/a	n/a
19	CTCF	chr3:121553600-121553750	GM12872	blood:	n/a	n/a
20	PML	chr3:121553663-121554276	GM12878	blood:	n/a	n/a
21	REST	chr3:121553326-121554543	H1-neurons	neurons:	n/a	chr3:121554444-121554453 chr3:121553613-121553626 chr3:121553507-121553514 chr3:121553523-121553543
22	RFX5	chr3:121553398-121554316	Hela-S3	cervix:	n/a	chr3:121553973-121553982
23	POLR2A	chr3:121552954-121554575	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:121553702-121554231	HepG2	liver:	n/a	n/a
25	BRCA1	chr3:121553701-121553956	HepG2	liver:	n/a	n/a
26	MAX	chr3:121553234-121554450	ECC-1	luminal epithelium:	n/a	chr3:121554359-121554369
27	POLR2A	chr3:121553347-121554311	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:121553356-121554400	Hela-S3	cervix:	n/a	n/a
29	STAT5A	chr3:121553201-121554481	GM12878	blood:	n/a	chr3:121554356-121554368 chr3:121554351-121554363 chr3:121554352-121554364 chr3:121554362-121554374
30	MXI1	chr3:121552793-121555264	SK-N-SH	brain:	n/a	n/a
31	PAX5	chr3:121553688-121554392	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:121553566-121554317	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr3:121553527-121554559	GM12878	blood:	n/a	n/a
34	JUND	chr3:121553443-121554492	H1-hESC	embryonic stem cell:	n/a	chr3:121554442-121554456 chr3:121553974-121553983
35	PML	chr3:121553169-121554615	GM12878	blood:	n/a	n/a
36	CREB1	chr3:121553489-121554376	HepG2	liver:	n/a	n/a
37	POLR2A	chr3:121553573-121554674	GM12892	blood:	n/a	n/a
38	TAF1	chr3:121553563-121554421	ECC-1	luminal epithelium:	n/a	n/a
39	POU2F2	chr3:121553676-121553951	GM12878	blood:	n/a	chr3:121553780-121553792
40	NFIC	chr3:121553627-121554071	HepG2	liver:	n/a	n/a
41	POLR2A	chr3:121552849-121554755	GM12891	blood:	n/a	n/a
42	TBP	chr3:121552987-121554274	Hela-S3	cervix:	n/a	n/a
43	SIN3AK20	chr3:121553574-121554330	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr3:121553653-121554295	A549	lung:	n/a	n/a
45	CHD2	chr3:121553694-121554658	GM12878	blood:	n/a	chr3:121554351-121554361
46	POLR2A	chr3:121553581-121554653	K562	blood:	n/a	n/a
47	E2F6	chr3:121553358-121554377	A549	lung:	n/a	chr3:121553581-121553588 chr3:121553903-121553914 chr3:121553581-121553588 chr3:121553581-121553588
48	MAX	chr3:121553215-121554213	SK-N-SH	brain:	n/a	n/a
49	MAX	chr3:121553438-121554385	HepG2	liver:	n/a	chr3:121554359-121554369
50	CTCF	chr3:121553640-121553790	HCM	heart:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:121465799..121468529-chr3:121552939..121555166,2	MCF-7	breast:
2	chr3:121466624..121468797-chr3:121553319..121555550,2	MCF-7	breast:
3	chr3:121552695..121555483-chr3:122101751..122103619,2	MCF-7	breast:
4	chr3:121552259..121553812-chr3:121688554..121691121,2	MCF-7	breast:

Variant related genes	Relation type
EAF2	TF binding region
ENSG00000173230	Chromatin interaction
ENSG00000114023	Chromatin interaction
ENSG00000160124	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10934560	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10934568	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12489511	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13067629	0.95[CEU][hapmap];0.92[CHB][hapmap]
rs17849995	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1919552	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1919557	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs2001391	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs2141614	1.00[JPT][hapmap]
rs2331963	0.83[MEX][hapmap]
rs2332056	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2700424	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs34227248	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34920680	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34980632	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35713885	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36022362	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3817599	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs4482697	0.83[MEX][hapmap]
rs4676690	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4676751	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676754	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57420306	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59740137	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6438660	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6438661	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6770719	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6771716	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6774164	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6776703	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6791510	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6802033	0.90[CEU][hapmap];0.84[CHB][hapmap]
rs6803839	0.95[CEU][hapmap];0.92[CHB][hapmap]
rs6807711	0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs73179983	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73181839	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7429247	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs7646346	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646585	0.95[CEU][hapmap];0.92[CHB][hapmap]
rs7652239	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289172	0.90[CEU][hapmap];0.84[CHB][hapmap]
rs9289173	0.90[CEU][hapmap];0.84[CHB][hapmap]
rs953730	0.80[GIH][hapmap]
rs9681049	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9681209	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9809114	0.90[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs9812411	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs9864907	0.90[CEU][hapmap];0.92[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv933192	chr3:121544496-121575871	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12490565	SLC15A2	cis	cerebellum	SCAN
rs12490565	SLC15A2	cis	parietal	SCAN
rs12490565	HCLS1	Cis_1M	lymphoblastoid	RTeQTL
rs12490565	ADPRH	cis	parietal	SCAN
rs12490565	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs12490565	MUC13	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121552000-121556600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:121552400-121554400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr3:121552600-121553800	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr3:121552600-121553800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr3:121552600-121553800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:121552600-121553800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:121552600-121554400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:121552800-121553800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr3:121552800-121553800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr3:121552800-121553800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:121552800-121553800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr3:121552800-121554000	Active TSS	Fetal Muscle Trunk	muscle
13	chr3:121552800-121554400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:121552800-121554600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:121552800-121554600	Active TSS	Gastric	stomach
16	chr3:121552800-121554800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr3:121552800-121554800	Active TSS	Aorta	Aorta
18	chr3:121552800-121554800	Active TSS	Colonic Mucosa	Colon
19	chr3:121552800-121554800	Active TSS	Placenta	Placenta
20	chr3:121552800-121554800	Active TSS	Left Ventricle	heart
21	chr3:121552800-121554800	Active TSS	Pancreas	Pancrea
22	chr3:121552800-121554800	Active TSS	Psoas Muscle	Psoas
23	chr3:121552800-121555200	Active TSS	Right Ventricle	heart
24	chr3:121552800-121555400	Active TSS	Right Atrium	heart
25	chr3:121553000-121553800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr3:121553000-121553800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr3:121553000-121553800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:121553000-121554200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:121553000-121554200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:121553000-121554400	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr3:121553000-121554400	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr3:121553000-121554400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:121553000-121554400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:121553000-121554400	Active TSS	Fetal Brain Female	brain
35	chr3:121553000-121554400	Active TSS	NHDF-Ad	bronchial
36	chr3:121553000-121554600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:121553000-121554600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:121553000-121554600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:121553000-121554600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:121553000-121554600	Active TSS	Brain Angular Gyrus	brain
41	chr3:121553000-121554800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:121553000-121554800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:121553000-121554800	Active TSS	Fetal Intestine Small	intestine
44	chr3:121553000-121554800	Active TSS	Ovary	ovary
45	chr3:121553000-121555000	Active TSS	Fetal Intestine Large	intestine
46	chr3:121553000-121555200	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:121553000-121555600	Active TSS	K562	blood
48	chr3:121553000-121556400	Active TSS	GM12878-XiMat	blood
49	chr3:121553200-121554200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr3:121553200-121554200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links