Variant report

Variant	rs862464
Chromosome Location	chr19:39345025-39345026
allele	A/G
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	chr19:39344847-39345047	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
HNRNPL	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1103435	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113123	0.91[EUR][1000 genomes]
rs2113124	0.89[EUR][1000 genomes]
rs2278009	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278011	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278012	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2318459	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508822	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67859595	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7246134	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255774	0.96[ASN][1000 genomes]
rs8104416	0.88[EUR][1000 genomes]
rs8104420	0.91[EUR][1000 genomes]
rs862455	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862459	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9789283	0.89[EUR][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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs862464	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL
rs862464	ECH1	Cis_1M	lymphoblastoid	RTeQTL
rs862464	HNRNPL	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39343600-39348200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:39343600-39359800	Weak transcription	Small Intestine	intestine
3	chr19:39343800-39345400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:39343800-39346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:39343800-39347200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:39343800-39347200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:39343800-39347400	Weak transcription	Primary T cells from cord blood	blood
8	chr19:39343800-39347400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:39343800-39347800	Weak transcription	Fetal Thymus	thymus
10	chr19:39343800-39348200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:39343800-39348200	Weak transcription	Esophagus	oesophagus
12	chr19:39343800-39348200	Weak transcription	HSMMtube	muscle
13	chr19:39343800-39352400	Weak transcription	HUVEC	blood vessel
14	chr19:39343800-39353000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr19:39343800-39353200	Weak transcription	Fetal Kidney	kidney
16	chr19:39344000-39345400	Enhancers	K562	blood
17	chr19:39344000-39346800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr19:39344000-39347000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:39344000-39347000	Weak transcription	Spleen	Spleen
20	chr19:39344000-39347200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:39344000-39347200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:39344000-39347200	Weak transcription	GM12878-XiMat	blood
23	chr19:39344000-39347400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:39344000-39347400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:39344000-39347400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:39344000-39347400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:39344000-39347400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr19:39344000-39347400	Weak transcription	A549	lung
29	chr19:39344000-39347400	Weak transcription	HepG2	liver
30	chr19:39344000-39347600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:39344000-39347600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr19:39344000-39347600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:39344000-39347600	Weak transcription	Adipose Nuclei	Adipose
34	chr19:39344000-39347600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr19:39344000-39347800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:39344000-39347800	Weak transcription	Osteobl	bone
37	chr19:39344000-39348200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:39344000-39348200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr19:39344000-39348200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:39344000-39352800	Weak transcription	Lung	lung
41	chr19:39344000-39353000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:39344000-39353000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:39344000-39353200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:39344000-39353200	Weak transcription	Right Atrium	heart
45	chr19:39344200-39346800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:39344200-39346800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:39344200-39347400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:39344200-39347800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr19:39344200-39347800	Weak transcription	Placenta	Placenta
50	chr19:39344200-39348200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links