Variant report

Variant	rs3786553
Chromosome Location	chr19:41902746-41902747
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	MYC	chr19:41902423-41905263	A549	lung:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
2	POU2F2	chr19:41902482-41902846	GM12891	blood:	n/a	chr19:41902685-41902700 chr19:41902683-41902701 chr19:41902688-41902697 chr19:41902689-41902696 chr19:41902686-41902697 chr19:41902686-41902699 chr19:41902688-41902696 chr19:41902687-41902697 chr19:41902688-41902698
3	EP300	chr19:41902731-41904208	A549	lung:	n/a	n/a
4	MAX	chr19:41902738-41904121	A549	lung:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
5	MXI1	chr19:41902656-41904646	IMR90	lung:	n/a	chr19:41903347-41903356
6	MXI1	chr19:41902249-41904351	SK-N-SH	brain:	n/a	chr19:41903347-41903356
7	RUNX3	chr19:41902489-41902810	GM12878	blood:	n/a	n/a
8	BCL3	chr19:41902714-41904265	A549	lung:	n/a	chr19:41903264-41903273 chr19:41903275-41903288
9	TCF12	chr19:41902735-41904415	A549	lung:	n/a	n/a
10	SIN3AK20	chr19:41902712-41904306	A549	lung:	n/a	n/a
11	MYC	chr19:41902568-41904114	MCF10A-Er-Src	breast:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
12	POU2F2	chr19:41902507-41902897	GM12878	blood:	n/a	chr19:41902685-41902700 chr19:41902683-41902701 chr19:41902688-41902697 chr19:41902689-41902696 chr19:41902686-41902697 chr19:41902686-41902699 chr19:41902688-41902696 chr19:41902687-41902697 chr19:41902688-41902698
13	SIN3AK20	chr19:41902677-41904214	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:41902746-41904078	SK-N-MC	brain:	n/a	n/a
15	MAX	chr19:41902622-41904412	A549	lung:	n/a	chr19:41903346-41903356 chr19:41903242-41903252 chr19:41903244-41903251 chr19:41903241-41903256 chr19:41903347-41903354 chr19:41903243-41903252 chr19:41903346-41903355 chr19:41903349-41903357 chr19:41903346-41903355
16	JUN	chr19:41902375-41904298	K562	blood:	n/a	n/a
17	SIX5	chr19:41902666-41904297	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41899828..41905293-chr19:41906916..41917787,16	MCF-7	breast:
2	chr19:41815990..41817853-chr19:41901729..41903326,2	K562	blood:
3	chr19:41868160..41870059-chr19:41902135..41903854,4	K562	blood:
4	chr19:41861983..41864638-chr19:41901106..41902845,2	K562	blood:
5	chr19:41856329..41860180-chr19:41901826..41904297,4	K562	blood:
6	chr19:41902636..41905103-chr19:41930716..41934044,4	MCF-7	breast:
7	chr19:41855447..41861218-chr19:41901143..41905435,7	MCF-7	breast:
8	chr19:41856174..41858570-chr19:41902142..41904818,3	MCF-7	breast:
9	chr19:41868160..41871597-chr19:41899998..41904284,10	K562	blood:
10	chr19:41868161..41871707-chr19:41902716..41905358,4	MCF-7	breast:
11	chr19:41901938..41905441-chr19:41944047..41947443,5	K562	blood:
12	chr19:41901991..41905119-chr19:41933008..41936084,3	MCF-7	breast:
13	chr19:41855237..41861298-chr19:41901562..41905286,5	K562	blood:
14	chr19:41902654..41904815-chr19:41927221..41929015,2	K562	blood:

Variant related genes	Relation type
BCKDHA	TF binding region
ENSG00000268987	TF binding region
ENSG00000142039	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000268475	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000255730	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10409485	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10413735	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10416743	0.97[ASN][1000 genomes]
rs10417311	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10417997	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420556	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10422783	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10422956	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10432268	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1043413	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1077856	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853751	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083618	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083619	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667848	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11667908	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11668924	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11670583	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670668	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670725	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11670757	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11880539	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11883104	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12602	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12709849	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12980966	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12982607	0.81[ASN][1000 genomes]
rs13344547	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13344563	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13345590	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13346603	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1473248	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs166925	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16975238	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17318596	0.88[ASN][1000 genomes]
rs17318666	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1967333	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1967334	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2231940	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241706	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241707	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241708	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241709	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241710	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241711	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288871	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304242	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2317131	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569400	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2569754	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284648	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284649	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284650	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284651	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284652	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284654	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284655	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284656	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284657	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284658	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs284660	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284661	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284662	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs284663	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3213860	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213861	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3745290	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745292	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810174	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810175	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3816037	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826713	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4605279	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4674	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802116	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802117	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802118	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803461	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803462	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803463	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803465	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803467	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803468	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803469	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55986560	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58961854	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62117461	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62117462	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508977	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7247332	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7255918	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7258973	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8103531	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8105450	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8105833	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878082	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs878083	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs892044	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9304593	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3786553	B3GNT8	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41883000-41902800	Weak transcription	Stomach Mucosa	stomach
2	chr19:41883200-41902800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:41883200-41902800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:41886400-41902800	Weak transcription	NHDF-Ad	bronchial
5	chr19:41897800-41902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:41898000-41902800	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:41898000-41902800	Weak transcription	NHLF	lung
8	chr19:41898200-41902800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:41898200-41902800	Weak transcription	Aorta	Aorta
10	chr19:41898200-41902800	Weak transcription	Left Ventricle	heart
11	chr19:41898200-41902800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:41898400-41902800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:41899200-41903000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:41899400-41902800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:41901000-41902800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:41901000-41902800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr19:41901200-41902800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr19:41901200-41903000	Enhancers	Spleen	Spleen
19	chr19:41901400-41902800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:41901400-41902800	Enhancers	Brain Angular Gyrus	brain
21	chr19:41901400-41903200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:41901600-41902800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr19:41901600-41903200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr19:41901600-41904000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:41901600-41904200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:41901800-41902800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:41901800-41903200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr19:41901800-41904400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:41902000-41902800	Enhancers	Placenta	Placenta
30	chr19:41902000-41902800	Weak transcription	Gastric	stomach
31	chr19:41902000-41902800	Weak transcription	Lung	lung
32	chr19:41902000-41904400	Active TSS	Hela-S3	cervix
33	chr19:41902000-41904600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:41902200-41902800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:41902200-41904400	Active TSS	H1 Cell Line	embryonic stem cell
36	chr19:41902200-41904400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:41902200-41904400	Active TSS	HSMM	muscle
38	chr19:41902200-41904600	Active TSS	Pancreas	Pancrea
39	chr19:41902200-41904600	Active TSS	GM12878-XiMat	blood
40	chr19:41902200-41904600	Active TSS	K562	blood
41	chr19:41902200-41905200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:41902400-41902800	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr19:41902400-41902800	Active TSS	Muscle Satellite Cultured Cells	--
44	chr19:41902400-41902800	Enhancers	Brain Substantia Nigra	brain
45	chr19:41902400-41902800	Enhancers	Fetal Heart	heart
46	chr19:41902400-41902800	Flanking Active TSS	Fetal Stomach	stomach
47	chr19:41902400-41902800	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr19:41902400-41902800	Enhancers	Rectal Smooth Muscle	rectum
49	chr19:41902400-41902800	Enhancers	HUVEC	blood vessel
50	chr19:41902400-41902800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links