Variant report

Variant	rs11881305
Chromosome Location	chr19:38804218-38804219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr19:38804176-38804449	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:38804110-38804539	K562	blood:	n/a	n/a
3	MYC	chr19:38804186-38804573	K562	blood:	n/a	chr19:38804553-38804564
4	ARID3A	chr19:38804182-38804600	K562	blood:	n/a	n/a
5	MAX	chr19:38804169-38804569	K562	blood:	n/a	chr19:38804553-38804564
6	EP300	chr19:38804077-38804593	K562	blood:	n/a	chr19:38804566-38804580
7	UBTF	chr19:38804193-38804554	K562	blood:	n/a	n/a
8	ZNF384	chr19:38803080-38804731	K562	blood:	n/a	n/a
9	ZMIZ1	chr19:38804216-38804452	K562	blood:	n/a	n/a
10	POLR2A	chr19:38804097-38804563	K562	blood:	n/a	n/a
11	POLR2A	chr19:38804093-38804372	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:38802749-38804772	K562	blood:	n/a	n/a
13	MYC	chr19:38804202-38804553	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUN	chr19:38804176-38804381	H1-hESC	embryonic stem cell:	n/a	n/a
15	PML	chr19:38804098-38804526	K562	blood:	n/a	n/a
16	MAX	chr19:38804117-38804590	H1-hESC	embryonic stem cell:	n/a	chr19:38804553-38804564
17	JUND	chr19:38804050-38804717	K562	blood:	n/a	n/a
18	HEY1	chr19:38804183-38804594	K562	blood:	n/a	n/a
19	MXI1	chr19:38804198-38804462	H1-hESC	embryonic stem cell:	n/a	n/a
20	ATF2	chr19:38804133-38804425	H1-hESC	embryonic stem cell:	n/a	n/a
21	ATF2	chr19:38804094-38804345	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr19:38804076-38804599	K562	blood:	n/a	n/a
23	SP1	chr19:38804103-38804415	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAFK	chr19:38804141-38804409	K562	blood:	n/a	n/a
25	TBL1XR1	chr19:38804196-38804547	K562	blood:	n/a	n/a
26	BACH1	chr19:38804215-38804375	H1-hESC	embryonic stem cell:	n/a	n/a
27	MYC	chr19:38804146-38804696	K562	blood:	n/a	chr19:38804553-38804564
28	TBP	chr19:38804171-38804488	K562	blood:	n/a	n/a
29	POLR2A	chr19:38804106-38804574	K562	blood:	n/a	n/a
30	POLR2A	chr19:38804216-38804603	K562	blood:	n/a	n/a
31	MAX	chr19:38804144-38804547	H1-hESC	embryonic stem cell:	n/a	n/a
32	JUND	chr19:38804133-38804408	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr19:38804039-38804581	K562	blood:	n/a	chr19:38804553-38804564

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38802009..38804221-chr19:38806405..38809236,2	K562	blood:
2	chr19:38803963..38805579-chr19:38834586..38836775,2	K562	blood:
3	chr19:38795298..38801659-chr19:38801673..38807893,10	K562	blood:

No data

Variant related genes	Relation type
YIF1B	TF binding region
ENSG00000167645	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12609247	0.89[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12611255	0.86[AMR][1000 genomes]
rs1821284	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2270095	1.00[ASW][hapmap];0.98[GIH][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs2286475	0.93[GIH][hapmap];0.95[TSI][hapmap]
rs2286476	0.81[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap]
rs2304176	0.96[GIH][hapmap];0.97[TSI][hapmap]
rs2891602	0.81[YRI][hapmap]
rs3178327	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35436012	0.86[EUR][1000 genomes]
rs3843754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4312417	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4802324	0.86[ASW][hapmap];0.83[CEU][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4803999	0.83[EUR][1000 genomes]
rs61160177	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71354995	0.94[EUR][1000 genomes]
rs7252835	0.85[AFR][1000 genomes]
rs7253960	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257537	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260137	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73043010	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs8112211	0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]

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	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
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11881305	APOC4	cis	cerebellum	SCAN
rs11881305	PSG4	cis	cerebellum	SCAN
rs11881305	SELV	cis	parietal	SCAN
rs11881305	C19orf33	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38771400-38805800	Weak transcription	Right Atrium	heart
2	chr19:38781200-38805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:38784000-38805800	Weak transcription	Primary B cells from cord blood	blood
5	chr19:38792000-38805400	Weak transcription	NHDF-Ad	bronchial
6	chr19:38792000-38805800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:38795200-38805800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:38795400-38805800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:38795600-38805800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:38796200-38804400	Weak transcription	NH-A	brain
11	chr19:38796200-38805400	Weak transcription	HepG2	liver
12	chr19:38796400-38805400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:38796400-38805600	Weak transcription	Hela-S3	cervix
14	chr19:38796400-38805800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:38796400-38805800	Weak transcription	HUVEC	blood vessel
16	chr19:38796600-38805600	Weak transcription	HMEC	breast
17	chr19:38796600-38805800	Weak transcription	Fetal Heart	heart
18	chr19:38796600-38805800	Weak transcription	Stomach Mucosa	stomach
19	chr19:38798200-38805800	Weak transcription	Small Intestine	intestine
20	chr19:38798400-38805800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:38798400-38805800	Weak transcription	Fetal Thymus	thymus
22	chr19:38798600-38805400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:38798600-38805800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:38798800-38805200	Weak transcription	HSMM	muscle
25	chr19:38798800-38805600	Weak transcription	HSMMtube	muscle
26	chr19:38799000-38805800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:38799200-38805600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr19:38799400-38805600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:38799400-38805800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:38799400-38805800	Weak transcription	Brain Substantia Nigra	brain
31	chr19:38799400-38805800	Weak transcription	Fetal Lung	lung
32	chr19:38799600-38805400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:38799600-38805400	Weak transcription	Osteobl	bone
34	chr19:38799600-38805600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:38799600-38805600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:38799600-38805600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:38799600-38805600	Weak transcription	Esophagus	oesophagus
38	chr19:38799600-38805800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:38799600-38805800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:38799600-38805800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:38799800-38805800	Weak transcription	Primary T cells from cord blood	blood
42	chr19:38800000-38805800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr19:38800000-38805800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr19:38800000-38805800	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:38800200-38804400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:38800200-38805400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:38800200-38805400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:38800200-38805400	Weak transcription	Fetal Muscle Leg	muscle
49	chr19:38800200-38805600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:38800200-38805600	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links