Variant report

Variant	rs1858844
Chromosome Location	chr19:36128988-36128989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36128908-36129563	K562	blood:	n/a	n/a
2	POLR2A	chr19:36128579-36129582	K562	blood:	n/a	n/a
3	POLR2A	chr19:36127361-36129687	K562	blood:	n/a	n/a
4	POLR2A	chr19:36128774-36129499	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:36128970-36129203	GM12878	blood:	n/a	n/a
6	ELF1	chr19:36128694-36128992	K562	blood:	n/a	chr19:36128831-36128844
7	POLR2A	chr19:36128678-36129180	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:36128465-36129006	K562	blood:	n/a	n/a
9	POLR2A	chr19:36128906-36129072	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:36128760-36129257	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:36128637-36129063	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:36128531-36129692	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:36128705-36129084	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:36128726-36129045	K562	blood:	n/a	n/a
15	POLR2A	chr19:36128128-36131051	K562	blood:	n/a	n/a
16	POLR2A	chr19:36128620-36129239	HL-60	blood:	n/a	n/a
17	POLR2A	chr19:36128618-36129771	GM12892	blood:	n/a	n/a
18	POLR2A	chr19:36128559-36130881	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:36128703-36131061	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr19:36128662-36129611	A549	lung:	n/a	n/a
21	POLR2A	chr19:36128840-36129572	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	chr19:36118444..36125285-chr19:36125367..36133017,11	MCF-7	breast:
2	chr19:36118572..36120760-chr19:36128325..36130152,2	MCF-7	breast:

No data

Variant related genes	Relation type
ETV2	TF binding region
ENSG00000126254	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10410294	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs10415676	0.83[ASN][1000 genomes]
rs10439089	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12461025	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1989801	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285413	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs3814983	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs3826999	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4447555	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6510501	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8100735	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106576	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107941	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8113090	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9304873	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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv911629	chr19:36122886-36136449	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1858844	CNFN	cis	cerebellum	SCAN
rs1858844	LTBP4	cis	parietal	SCAN
rs1858844	TMEM91	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36120600-36129800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:36120800-36129600	Strong transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:36120800-36132400	Weak transcription	Fetal Heart	heart
4	chr19:36120800-36134000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:36121000-36129000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:36121000-36129600	Strong transcription	Fetal Stomach	stomach
7	chr19:36121200-36129000	Strong transcription	Adipose Nuclei	Adipose
8	chr19:36121200-36129200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:36121200-36129200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr19:36121200-36129400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:36121200-36129400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:36121200-36129400	Strong transcription	Liver	Liver
13	chr19:36121200-36129600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:36121200-36129600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:36121200-36129600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr19:36121200-36129600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:36121200-36129600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:36121200-36129600	Strong transcription	Fetal Thymus	thymus
19	chr19:36121400-36129000	Strong transcription	Colonic Mucosa	Colon
20	chr19:36121400-36129000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr19:36121400-36129200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:36121400-36129200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr19:36121400-36129200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:36121400-36129400	Strong transcription	Fetal Muscle Leg	muscle
25	chr19:36121400-36129600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:36121400-36129600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:36121400-36129600	Strong transcription	Fetal Intestine Large	intestine
28	chr19:36121400-36129600	Strong transcription	Fetal Intestine Small	intestine
29	chr19:36121600-36129000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:36121600-36129000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:36121600-36129000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:36121600-36129000	Strong transcription	Colon Smooth Muscle	Colon
33	chr19:36121600-36129000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr19:36121600-36129200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr19:36121600-36129200	Strong transcription	Ovary	ovary
36	chr19:36121600-36129200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:36121600-36129400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:36121600-36129400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:36121600-36129400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:36121600-36129400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr19:36121600-36129400	Strong transcription	Primary T cells from cord blood	blood
42	chr19:36121600-36129400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:36121600-36129400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:36121600-36129400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:36121600-36129400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr19:36121600-36129400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:36121600-36129400	Strong transcription	Left Ventricle	heart
48	chr19:36121600-36129400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr19:36121600-36129400	Strong transcription	HepG2	liver
50	chr19:36121600-36129400	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links