Variant report

Variant	rs11556992
Chromosome Location	chr19:38800176-38800177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38799731-38800571	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:38799815-38800268	ECC-1	luminal epithelium:	n/a	n/a
3	PBX3	chr19:38797539-38800611	A549	lung:	n/a	n/a
4	ELF1	chr19:38799710-38800498	A549	lung:	n/a	n/a
5	POLR2A	chr19:38797503-38800847	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:38798569-38800748	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr19:38797752-38800533	A549	lung:	n/a	n/a
8	GATA3	chr19:38797920-38800625	A549	lung:	n/a	n/a
9	POLR2A	chr19:38797757-38800463	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr19:38799791-38800433	MCF-7	breast:	n/a	n/a
11	POLR2A	chr19:38797681-38802572	A549	lung:	n/a	n/a
12	POLR2A	chr19:38797538-38800450	HCT-116	colon:	n/a	n/a
13	POLR2A	chr19:38797826-38800468	Hela-S3	cervix:	n/a	n/a
14	TCF12	chr19:38797470-38800431	A549	lung:	n/a	chr19:38799081-38799088
15	PBX3	chr19:38797530-38800714	A549	lung:	n/a	n/a
16	JUND	chr19:38797688-38800894	A549	lung:	n/a	n/a
17	BCL3	chr19:38797589-38800656	A549	lung:	n/a	n/a
18	POLR2A	chr19:38799403-38800465	A549	lung:	n/a	n/a
19	POLR2A	chr19:38797721-38800561	A549	lung:	n/a	n/a
20	POLR2A	chr19:38798607-38800211	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr19:38797487-38801981	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr19:38797631-38800363	HCT-116	colon:	n/a	n/a
23	POLR2A	chr19:38799587-38800420	A549	lung:	n/a	n/a
24	BCL3	chr19:38798688-38800758	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38796381..38798650-chr19:38799992..38801610,2	K562	blood:
2	chr19:38800007..38802686-chr19:38805252..38808238,5	K562	blood:
3	chr19:38795298..38801659-chr19:38801673..38807893,10	K562	blood:
4	chr19:38755064..38756730-chr19:38799714..38801909,2	MCF-7	breast:
5	chr19:38794669..38796308-chr19:38799482..38801247,2	K562	blood:

No data

Variant related genes	Relation type
YIF1B	TF binding region
ENSG00000167642	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000167644	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12609258	0.81[ASN][1000 genomes]
rs12610650	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2060244	0.83[AFR][1000 genomes]
rs2074982	0.83[CHD][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2286474	0.81[ASN][1000 genomes]
rs2384783	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2891602	0.96[GIH][hapmap];0.90[TSI][hapmap]
rs3745949	0.83[AFR][1000 genomes]
rs3745954	0.85[JPT][hapmap];0.81[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

No data

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	chr19:38794400-38800200	Strong transcription	Brain Inferior Temporal Lobe	brain
8	chr19:38794400-38800400	Strong transcription	Aorta	Aorta
9	chr19:38794400-38800400	Strong transcription	Thymus	Thymus
10	chr19:38794400-38800400	Strong transcription	NHLF	lung
11	chr19:38794800-38800400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:38795200-38800600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:38795200-38805800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:38795400-38800200	Strong transcription	Brain Germinal Matrix	brain
15	chr19:38795400-38800400	Strong transcription	Dnd41	blood
16	chr19:38795400-38800600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr19:38795400-38800600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:38795400-38805800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr19:38795600-38800800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:38795600-38805800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr19:38795800-38800800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:38795800-38801800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:38796000-38800400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:38796000-38800400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38796000-38800400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:38796000-38803400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:38796200-38800200	Strong transcription	Liver	Liver
28	chr19:38796200-38804400	Weak transcription	NH-A	brain
29	chr19:38796200-38805400	Weak transcription	HepG2	liver
30	chr19:38796400-38800200	Strong transcription	Fetal Muscle Leg	muscle
31	chr19:38796400-38800400	Strong transcription	Adipose Nuclei	Adipose
32	chr19:38796400-38800800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr19:38796400-38801600	Strong transcription	Fetal Stomach	stomach
34	chr19:38796400-38801800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:38796400-38803200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:38796400-38805400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:38796400-38805600	Weak transcription	Hela-S3	cervix
38	chr19:38796400-38805800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr19:38796400-38805800	Weak transcription	HUVEC	blood vessel
40	chr19:38796600-38800400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:38796600-38802400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:38796600-38805600	Weak transcription	HMEC	breast
43	chr19:38796600-38805800	Weak transcription	Fetal Heart	heart
44	chr19:38796600-38805800	Weak transcription	Stomach Mucosa	stomach
45	chr19:38796800-38800400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:38796800-38802400	Strong transcription	Brain Hippocampus Middle	brain
47	chr19:38797000-38800200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:38797000-38800200	Strong transcription	Brain Anterior Caudate	brain
49	chr19:38797000-38800400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:38797000-38800400	Strong transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links