Variant report

Variant	rs11539797
Chromosome Location	chr19:41939497-41939498
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	POLR2A	chr19:41936242-41939720	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41939184-41939736	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:41939045-41939564	A549	lung:	n/a	n/a
4	POLR2A	chr19:41939070-41939506	GM12891	blood:	n/a	n/a
5	STAT5A	chr19:41938169-41939538	GM12878	blood:	n/a	chr19:41939348-41939360
6	POLR2A	chr19:41939266-41939588	K562	blood:	n/a	n/a
7	POLR2A	chr19:41939050-41939651	HL-60	blood:	n/a	n/a
8	POLR2A	chr19:41939040-41939737	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr19:41939020-41939616	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr19:41936772-41939698	K562	blood:	n/a	n/a
11	POLR2A	chr19:41938965-41939773	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41936622..41939586-chr19:41947612..41949294,2	K562	blood:
2	chr19:41932057..41934259-chr19:41937890..41940958,3	MCF-7	breast:

Variant related genes	Relation type
B3GNT8	TF binding region
ENSG00000177191	Chromatin interaction
ENSG00000204978	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10406198	0.91[AFR][1000 genomes]
rs10407077	0.91[AFR][1000 genomes]
rs10409823	1.00[AFR][1000 genomes]
rs10410282	1.00[AFR][1000 genomes]
rs10410801	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10415116	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10418899	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs10419188	0.83[AFR][1000 genomes]
rs10425351	1.00[AFR][1000 genomes]
rs13343330	0.91[AFR][1000 genomes]
rs13346881	1.00[AFR][1000 genomes]
rs2231933	1.00[ASW][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2231938	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11539797	LYPD4	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41934000-41944800	Weak transcription	Hela-S3	cervix
2	chr19:41934400-41939600	Strong transcription	Brain Germinal Matrix	brain
3	chr19:41934400-41945000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:41934600-41944200	Weak transcription	Fetal Brain Male	brain
5	chr19:41934800-41939600	Strong transcription	Fetal Brain Female	brain
6	chr19:41934800-41945400	Weak transcription	Small Intestine	intestine
7	chr19:41935000-41940000	Strong transcription	Fetal Stomach	stomach
8	chr19:41935000-41945000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:41936200-41940000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:41936400-41939600	Strong transcription	Dnd41	blood
11	chr19:41936400-41939800	Strong transcription	NHEK	skin
12	chr19:41936600-41939600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:41936600-41939600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr19:41936600-41939600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr19:41936600-41939800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:41936600-41940600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:41936600-41944200	Strong transcription	A549	lung
18	chr19:41936800-41939600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr19:41936800-41939600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:41936800-41939600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:41936800-41939600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:41936800-41939600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:41936800-41939600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:41936800-41939600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:41936800-41939600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:41936800-41939600	Strong transcription	Colon Smooth Muscle	Colon
27	chr19:41936800-41939600	Strong transcription	Fetal Thymus	thymus
28	chr19:41936800-41939600	Strong transcription	Gastric	stomach
29	chr19:41936800-41939600	Strong transcription	Pancreas	Pancrea
30	chr19:41936800-41939800	Strong transcription	Adipose Nuclei	Adipose
31	chr19:41936800-41939800	Strong transcription	Placenta	Placenta
32	chr19:41936800-41939800	Strong transcription	Spleen	Spleen
33	chr19:41936800-41940000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr19:41936800-41940400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:41936800-41940600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:41936800-41944200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:41936800-41944200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:41936800-41944200	Strong transcription	Primary T cells from cord blood	blood
39	chr19:41937000-41939600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:41937000-41939600	Genic enhancers	Right Ventricle	heart
41	chr19:41937000-41939800	Strong transcription	Lung	lung
42	chr19:41937000-41940000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:41937000-41944200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr19:41937200-41939600	Strong transcription	Brain Hippocampus Middle	brain
45	chr19:41937200-41944200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:41937400-41939600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:41937400-41939600	Strong transcription	Ovary	ovary
48	chr19:41937400-41939600	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:41937600-41939600	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr19:41937600-41939600	Strong transcription	Primary T cells fromperipheralblood	blood

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