Variant report

Variant	rs3741499
Chromosome Location	chr12:56474379-56474380
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	EP300	chr12:56472579-56474424	ECC-1	luminal epithelium:	n/a	chr12:56472949-56472965 chr12:56472948-56472964 chr12:56473343-56473352 chr12:56472872-56472881
2	MAX	chr12:56472501-56474945	ECC-1	luminal epithelium:	n/a	chr12:56473390-56473397
3	TCF12	chr12:56472530-56474915	ECC-1	luminal epithelium:	n/a	chr12:56474487-56474496 chr12:56473236-56473243 chr12:56474467-56474477
4	POLR2A	chr12:56473778-56475011	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:56472756-56474740	H1-hESC	embryonic stem cell:	n/a	n/a
6	CREB1	chr12:56473476-56475162	HepG2	liver:	n/a	n/a
7	TEAD4	chr12:56472594-56474477	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr12:56472759-56474426	MCF-7	breast:	n/a	n/a
9	JUN	chr12:56472560-56475297	K562	blood:	n/a	chr12:56473840-56473849 chr12:56474554-56474563 chr12:56473309-56473318
10	ZBTB7A	chr12:56474206-56474835	K562	blood:	n/a	chr12:56474769-56474778
11	FOXA1	chr12:56474227-56475119	HepG2	liver:	n/a	n/a
12	E2F6	chr12:56473724-56474788	H1-hESC	embryonic stem cell:	n/a	chr12:56474766-56474776 chr12:56474274-56474284 chr12:56474737-56474746 chr12:56473864-56473875 chr12:56474519-56474531 chr12:56473828-56473837 chr12:56474254-56474263
13	ZBTB7A	chr12:56472728-56474839	ECC-1	luminal epithelium:	n/a	chr12:56474035-56474043 chr12:56473827-56473836 chr12:56474769-56474778
14	SP1	chr12:56474317-56475002	HepG2	liver:	n/a	chr12:56474552-56474566 chr12:56474503-56474517 chr12:56474443-56474456 chr12:56474465-56474479
15	ZBTB7A	chr12:56474186-56474630	K562	blood:	n/a	n/a
16	FOXA1	chr12:56474233-56474996	HepG2	liver:	n/a	n/a
17	SIN3AK20	chr12:56472473-56475252	MCF-7	breast:	n/a	n/a
18	TAF1	chr12:56473587-56474915	HepG2	liver:	n/a	n/a
19	POLR2A	chr12:56474287-56477511	HepG2	liver:	n/a	n/a
20	MAZ	chr12:56472653-56474409	IMR90	lung:	n/a	chr12:56473390-56473397
21	CEBPD	chr12:56474344-56474939	HepG2	liver:	n/a	n/a
22	CEBPB	chr12:56474315-56474987	HepG2	liver:	n/a	n/a
23	FOXA1	chr12:56474350-56475011	HepG2	liver:	n/a	n/a
24	ZBTB7A	chr12:56472522-56475010	ECC-1	luminal epithelium:	n/a	chr12:56474035-56474043 chr12:56473827-56473836 chr12:56474769-56474778
25	TAF1	chr12:56472638-56474380	ECC-1	luminal epithelium:	n/a	n/a
26	HEY1	chr12:56473273-56476974	HepG2	liver:	n/a	chr12:56475908-56475917 chr12:56473338-56473353 chr12:56474557-56474572
27	MXI1	chr12:56472724-56474916	HepG2	liver:	n/a	n/a
28	MAX	chr12:56472525-56475103	MCF-7	breast:	n/a	chr12:56473390-56473397
29	MAZ	chr12:56472732-56474884	K562	blood:	n/a	chr12:56473390-56473397
30	POLR2A	chr12:56472708-56474408	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr12:56472668-56474887	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr12:56472599-56474868	ECC-1	luminal epithelium:	n/a	chr12:56473390-56473397
33	HEY1	chr12:56472632-56476252	HepG2	liver:	n/a	chr12:56475908-56475917 chr12:56473338-56473353 chr12:56474557-56474572
34	REST	chr12:56474346-56474982	HepG2	liver:	n/a	n/a
35	TEAD4	chr12:56472552-56474565	ECC-1	luminal epithelium:	n/a	n/a
36	MAX	chr12:56473500-56474736	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr12:56472589-56474455	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr12:56473465-56474815	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTBP2	chr12:56472739-56474618	H1-hESC	embryonic stem cell:	n/a	n/a
40	ZBTB7A	chr12:56474371-56474887	HepG2	liver:	n/a	chr12:56474769-56474778
41	POLR2A	chr12:56472840-56476753	HepG2	liver:	n/a	n/a
42	ZEB1	chr12:56473842-56474400	GM12878	blood:	n/a	chr12:56474195-56474206
43	MYBL2	chr12:56473597-56475014	HepG2	liver:	n/a	n/a
44	YY1	chr12:56473560-56474813	HepG2	liver:	n/a	chr12:56473825-56473839 chr12:56474215-56474229 chr12:56474254-56474263
45	POLR2A	chr12:56472754-56474951	MCF-7	breast:	n/a	n/a
46	POLR2A	chr12:56473297-56476833	HepG2	liver:	n/a	n/a
47	GTF2F1	chr12:56473943-56474419	H1-hESC	embryonic stem cell:	n/a	n/a
48	TAF1	chr12:56473659-56474850	HepG2	liver:	n/a	n/a
49	POLR2A	chr12:56472467-56475271	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr12:56473325-56476141	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56318215..56321869-chr12:56472079..56475131,3	MCF-7	breast:
2	chr12:56320958..56322490-chr12:56473085..56475455,2	MCF-7	breast:
3	chr12:56210626..56213378-chr12:56473835..56475955,2	MCF-7	breast:
4	chr12:56471198..56482935-chr12:56506922..56516262,73	MCF-7	breast:
5	chr12:56115014..56117802-chr12:56474351..56476164,2	MCF-7	breast:
6	chr12:56471261..56483436-chr12:56494778..56506435,58	MCF-7	breast:
7	chr12:56473848..56475749-chr15:50645471..50647773,2	MCF-7	breast:
8	chr12:56390252..56392502-chr12:56472754..56475150,2	MCF-7	breast:
9	chr12:56319967..56322287-chr12:56473106..56474816,2	K562	blood:
10	chr12:56473891..56477008-chr12:56583227..56585798,3	MCF-7	breast:
11	chr12:56471332..56475358-chr12:56550630..56554454,5	MCF-7	breast:
12	chr12:56223221..56225412-chr12:56473813..56476164,2	MCF-7	breast:
13	chr12:56471831..56474623-chr12:56543968..56546467,2	K562	blood:
14	chr12:56435072..56437678-chr12:56471264..56476125,12	MCF-7	breast:
15	chr12:56473421..56475215-chr12:56613648..56616195,2	MCF-7	breast:
16	chr12:56473103..56475967-chr12:56549779..56553082,5	MCF-7	breast:
17	chr12:56434525..56442579-chr12:56471686..56475431,10	K562	blood:
18	chr12:56471798..56475584-chr12:56544179..56549010,6	MCF-7	breast:
19	chr12:56473548..56475475-chr12:56582788..56585025,2	K562	blood:
20	chr12:56472058..56475455-chr12:56477194..56480758,7	K562	blood:
21	chr12:56473182..56475897-chr12:56486719..56489015,2	K562	blood:
22	chr11:1591819..1593774-chr12:56472377..56474644,2	MCF-7	breast:
23	chr12:56473732..56475652-chr12:57482023..57483860,2	MCF-7	breast:
24	chr12:56470948..56480058-chr12:56507665..56513741,17	K562	blood:
25	chr12:56471914..56476515-chr12:56581933..56586574,4	MCF-7	breast:
26	chr12:56473664..56475878-chr12:56486736..56489717,2	MCF-7	breast:
27	chr12:56363280..56366159-chr12:56473026..56475603,2	MCF-7	breast:
28	chr12:56360952..56363260-chr12:56474163..56475825,2	MCF-7	breast:
29	chr12:56434525..56442579-chr12:56469196..56475242,12	K562	blood:
30	chr12:56209963..56212805-chr12:56473917..56475602,2	MCF-7	breast:
31	chr12:56471291..56475668-chr12:56497220..56500908,8	K562	blood:
32	chr12:56473597..56475914-chr12:56490066..56491584,2	MCF-7	breast:
33	chr12:56434164..56442518-chr12:56471459..56476251,24	MCF-7	breast:
34	chr12:56473857..56474425-chr12:56651625..56652490,2	K562	blood:
35	chr12:56472620..56475817-chr12:56544405..56546973,4	MCF-7	breast:
36	chr12:56472197..56476808-chr12:56477200..56483474,8	K562	blood:
37	chr12:56367265..56369715-chr12:56472830..56474688,3	MCF-7	breast:

Variant related genes	Relation type
ERBB3	TF binding region
ENSG00000065361	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000233930	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135437	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000184545	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000182796	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10876864	0.94[JPT][hapmap]
rs10876866	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10876870	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs11171739	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1131017	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1701704	0.86[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs1702877	0.81[EUR][1000 genomes]
rs2271194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2292239	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2456973	0.86[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs2640562	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2640564	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34415530	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4759229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61938962	0.86[EUR][1000 genomes]
rs61938963	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs705696	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs705704	0.86[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7297175	0.91[ASN][1000 genomes]
rs7302200	0.85[EUR][1000 genomes]
rs7305461	0.81[JPT][hapmap]
rs7312770	0.92[ASN][1000 genomes]
rs772921	0.86[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs773107	0.82[CEU][hapmap]
rs773109	0.82[JPT][hapmap]
rs7971751	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs877636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3741499	RAB5B	cis	Muscle Skeletal	GTEx
rs3741499	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs3741499	SUOX	cis	cerebellum	SCAN
rs3741499	SMARCC2	cis	parietal	SCAN
rs3741499	DEFB124	trans	lymphoblastoid	RTeQTL
rs3741499	AC034102.1	cis	Muscle Skeletal	GTEx
rs3741499	KRT82	cis	parietal	SCAN
rs3741499	MYL6B	cis	cerebellum	SCAN
rs3741499	TAC3	cis	parietal	SCAN
rs3741499	SUOX	cis	Thyroid	GTEx
rs3741499	CSRNP2	cis	parietal	SCAN
rs3741499	RPS26	cis	multi-tissue	Pritchard
rs3741499	SUOX	cis	parietal	SCAN
rs3741499	RPS26	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56472400-56474800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr12:56472400-56475000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:56472600-56474600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr12:56472600-56474600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:56472600-56474600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:56472600-56474600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:56472600-56474800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:56472600-56474800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:56472600-56475000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr12:56472600-56475200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:56472600-56475600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:56472600-56476000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:56472600-56477400	Active TSS	Brain Cingulate Gyrus	brain
14	chr12:56472800-56474400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr12:56472800-56474400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
16	chr12:56472800-56474400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:56472800-56474400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr12:56472800-56474400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:56472800-56474600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:56472800-56474600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
21	chr12:56472800-56474600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
22	chr12:56472800-56474600	Flanking Active TSS	HMEC	breast
23	chr12:56472800-56474600	Active TSS	NHEK	skin
24	chr12:56472800-56474800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr12:56472800-56474800	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr12:56472800-56474800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:56472800-56474800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr12:56472800-56475000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:56472800-56475000	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr12:56472800-56475000	Active TSS	Placenta Amnion	Placenta Amnion
31	chr12:56472800-56475400	Active TSS	Pancreas	Pancrea
32	chr12:56472800-56475800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr12:56472800-56476200	Active TSS	Fetal Kidney	kidney
34	chr12:56472800-56477400	Active TSS	Brain Substantia Nigra	brain
35	chr12:56473000-56474400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:56473000-56474400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:56473000-56474400	Bivalent Enhancer	Fetal Brain Male	brain
38	chr12:56473000-56474600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
39	chr12:56473000-56474600	Active TSS	Stomach Mucosa	stomach
40	chr12:56473000-56474600	Flanking Bivalent TSS/Enh	Thymus	Thymus
41	chr12:56473000-56475000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr12:56473000-56475600	Active TSS	Gastric	stomach
43	chr12:56473000-56475600	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr12:56473000-56475600	Active TSS	Small Intestine	intestine
45	chr12:56473000-56477400	Active TSS	Brain Angular Gyrus	brain
46	chr12:56473200-56474400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:56473200-56474800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:56473200-56474800	Flanking Bivalent TSS/Enh	Dnd41	blood
49	chr12:56473200-56476800	Active TSS	Rectal Smooth Muscle	rectum
50	chr12:56473400-56474400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links