Variant report

Variant	rs56101381
Chromosome Location	chr19:41272902-41272903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41270797-41272992	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:41268169-41273504	K562	blood:	n/a	n/a
3	POLR2A	chr19:41272731-41272979	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:41272769-41272968	K562	blood:	n/a	n/a
5	NFATC1	chr19:41272617-41273031	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:41272773-41272957	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:41271514-41273408	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr19:41271137-41272961	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:41270469-41273537	K562	blood:	n/a	n/a
10	BCL3	chr19:41272448-41273607	A549	lung:	n/a	n/a
11	POLR2A	chr19:41272759-41272954	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:41272652-41272951	GM12891	blood:	n/a	n/a
13	POLR2A	chr19:41271302-41273341	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:41271326-41273137	A549	lung:	n/a	n/a
15	POLR2A	chr19:41271331-41273326	HL-60	blood:	n/a	n/a
16	POLR2A	chr19:41272698-41272941	A549	lung:	n/a	n/a
17	POLR2A	chr19:41271325-41274974	HepG2	liver:	n/a	n/a
18	MTA3	chr19:41272584-41273238	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:41271310-41274003	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr19:41271856-41273239	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr19:41271360-41272945	K562	blood:	n/a	n/a
22	POLR2A	chr19:41271445-41273362	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr19:41272632-41273046	HL-60	blood:	n/a	n/a
24	POLR2A	chr19:41272666-41273050	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:41272751-41272966	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:41271662-41273215	K562	blood:	n/a	n/a
27	POLR2A	chr19:41272890-41272912	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:41272757-41272928	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:41272588-41272948	GM12891	blood:	n/a	n/a
30	POLR2A	chr19:41272573-41272965	GM12892	blood:	n/a	n/a
31	POLR2A	chr19:41272688-41272908	Hela-S3	cervix:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41271309..41273380-chr19:41283052..41284575,2	MCF-7	breast:
2	chr19:41271869..41274092-chr19:41280828..41283092,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIA-RAB4B	TF binding region
MIA	TF binding region
ENSG00000167578	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000171570	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10403040	0.96[EUR][1000 genomes]
rs10404944	0.87[AFR][1000 genomes]
rs10405596	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10405633	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10411008	0.96[EUR][1000 genomes]
rs10412175	0.90[AFR][1000 genomes]
rs10413760	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10416308	0.82[EUR][1000 genomes]
rs17713068	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2233152	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287691	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287692	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28660501	0.93[EUR][1000 genomes]
rs3875144	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
2	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
3	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41259000-41275200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41260600-41277200	Strong transcription	Fetal Brain Female	brain
4	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:41261200-41273000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:41261200-41273600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:41261600-41275000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:41261600-41275200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr19:41261800-41276800	Strong transcription	Fetal Intestine Small	intestine
10	chr19:41261800-41278200	Strong transcription	Fetal Stomach	stomach
11	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
12	chr19:41262000-41273400	Strong transcription	Brain Germinal Matrix	brain
13	chr19:41262000-41276200	Strong transcription	Thymus	Thymus
14	chr19:41262200-41273800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:41262400-41273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:41262600-41273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:41262600-41273000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:41262600-41273600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:41262600-41273600	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr19:41262800-41273000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr19:41262800-41275200	Strong transcription	Liver	Liver
22	chr19:41263000-41273000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:41263000-41273200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:41263000-41273400	Strong transcription	Lung	lung
25	chr19:41263000-41273800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:41263000-41273800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:41263000-41273800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr19:41263000-41274000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:41263200-41273200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr19:41263200-41273200	Strong transcription	Fetal Muscle Leg	muscle
31	chr19:41263200-41273400	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr19:41263200-41273600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:41263400-41273200	Strong transcription	HepG2	liver
34	chr19:41263400-41273400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:41263400-41273800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:41263400-41274000	Strong transcription	Colonic Mucosa	Colon
37	chr19:41263400-41275200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr19:41264600-41278000	Strong transcription	A549	lung
39	chr19:41265800-41273000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:41266000-41273000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:41269800-41273200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:41270000-41273800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:41270400-41282600	Weak transcription	Fetal Brain Male	brain
44	chr19:41271800-41273400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr19:41271800-41273600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr19:41271800-41275200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr19:41271800-41276800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:41271800-41279800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:41271800-41279800	Weak transcription	HMEC	breast
50	chr19:41271800-41282600	Weak transcription	Fetal Kidney	kidney

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