Variant report

Variant	rs4499346
Chromosome Location	chr19:39319018-39319019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39308463..39311353-chr19:39317850..39319477,2	MCF-7	breast:
2	chr19:39316681..39320266-chr19:39320279..39323590,5	K562	blood:

Variant related genes	Relation type
ENSG00000268756	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10413482	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10417798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853721	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052164	0.91[ASN][1000 genomes]
rs4801905	0.92[EUR][1000 genomes]
rs4801906	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55797435	0.89[EUR][1000 genomes]
rs56359606	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57195546	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59983525	0.91[ASN][1000 genomes]
rs60637521	0.93[EUR][1000 genomes]
rs61148075	0.83[EUR][1000 genomes]
rs61747761	0.86[EUR][1000 genomes]
rs73930204	0.89[EUR][1000 genomes]
rs73930206	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73933062	0.82[EUR][1000 genomes]
rs73933065	0.83[EUR][1000 genomes]
rs8111670	0.86[EUR][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	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	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4499346	HNRNPL	N/A	lymphoblastoid	RTeQTL
rs4499346	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39301400-39320200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr19:39304400-39321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:39304800-39320800	Weak transcription	HSMM	muscle
4	chr19:39305200-39321600	Strong transcription	Fetal Stomach	stomach
5	chr19:39305400-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:39305600-39320400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:39305600-39321000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:39307400-39321800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:39308200-39320400	Weak transcription	NHLF	lung
10	chr19:39309000-39320400	Weak transcription	Hela-S3	cervix
11	chr19:39310400-39321600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:39311800-39321200	Weak transcription	Stomach Mucosa	stomach
13	chr19:39311800-39321400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:39312600-39319800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr19:39312600-39320800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:39313600-39319200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr19:39313800-39319400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr19:39313800-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:39314000-39321400	Weak transcription	Esophagus	oesophagus
20	chr19:39315200-39321200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:39315400-39319800	Genic enhancers	Fetal Intestine Small	intestine
22	chr19:39315600-39321000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:39316000-39321400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:39316000-39321600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:39316200-39319600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:39316200-39320600	Strong transcription	Brain Germinal Matrix	brain
27	chr19:39316200-39321400	Genic enhancers	Placenta	Placenta
28	chr19:39316400-39319200	Strong transcription	Brain Anterior Caudate	brain
29	chr19:39316400-39319600	Strong transcription	Primary T cells from cord blood	blood
30	chr19:39316400-39320600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:39316600-39320400	Weak transcription	NHDF-Ad	bronchial
32	chr19:39316600-39320600	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr19:39316600-39321200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:39316600-39321400	Strong transcription	Fetal Lung	lung
35	chr19:39316600-39321600	Weak transcription	HUVEC	blood vessel
36	chr19:39316800-39320800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr19:39317000-39319200	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr19:39317200-39321000	Strong transcription	Thymus	Thymus
39	chr19:39317600-39319200	Strong transcription	HSMMtube	muscle
40	chr19:39317600-39320800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:39317600-39320800	Strong transcription	Fetal Thymus	thymus
42	chr19:39317600-39321000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:39317800-39319600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:39317800-39319800	Strong transcription	Brain Substantia Nigra	brain
45	chr19:39317800-39319800	Strong transcription	A549	lung
46	chr19:39317800-39320400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:39317800-39320800	Strong transcription	Dnd41	blood
48	chr19:39317800-39321000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:39317800-39321200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr19:39317800-39321400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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