Variant report

Variant	rs57195546
Chromosome Location	chr19:39318105-39318106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39316492..39318849-chr19:39371943..39374537,2	K562	blood:
2	chr19:39315714..39318484-chr19:39324884..39327703,2	K562	blood:
3	chr19:39308463..39311353-chr19:39317850..39319477,2	MCF-7	breast:
4	chr19:39316681..39320266-chr19:39320279..39323590,5	K562	blood:

Variant related genes	Relation type
ENSG00000268756	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10413482	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10417798	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10853721	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12052164	0.97[ASN][1000 genomes]
rs4499346	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4801905	0.96[EUR][1000 genomes]
rs4801906	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797435	0.89[EUR][1000 genomes]
rs56359606	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59089213	0.84[AFR][1000 genomes]
rs59983525	0.97[ASN][1000 genomes]
rs60637521	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61148075	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61747761	0.90[EUR][1000 genomes]
rs73930204	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73930206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73930207	0.84[AFR][1000 genomes]
rs73933062	0.87[EUR][1000 genomes]
rs73933063	0.84[AFR][1000 genomes]
rs73933065	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][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
rs57195546	HNRNPL	N/A	lymphoblastoid	RTeQTL
rs57195546	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	chr19:39284000-39318200	Weak transcription	Fetal Kidney	kidney
2	chr19:39296200-39318200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39296400-39318200	Weak transcription	NHEK	skin
4	chr19:39301400-39320200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr19:39304400-39321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:39304600-39318200	Weak transcription	Osteobl	bone
7	chr19:39304800-39320800	Weak transcription	HSMM	muscle
8	chr19:39305200-39321600	Strong transcription	Fetal Stomach	stomach
9	chr19:39305400-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:39305600-39318800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr19:39305600-39320400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:39305600-39321000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:39307400-39321800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:39308200-39320400	Weak transcription	NHLF	lung
15	chr19:39308400-39318200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:39308800-39318200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:39309000-39318200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:39309000-39320400	Weak transcription	Hela-S3	cervix
19	chr19:39310400-39321600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:39311800-39321200	Weak transcription	Stomach Mucosa	stomach
21	chr19:39311800-39321400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr19:39312600-39318400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:39312600-39319800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr19:39312600-39320800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:39313400-39318200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:39313600-39319200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr19:39313800-39319400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr19:39313800-39321000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:39314000-39318200	Weak transcription	GM12878-XiMat	blood
30	chr19:39314000-39321400	Weak transcription	Esophagus	oesophagus
31	chr19:39314200-39318200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr19:39315200-39321200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:39315400-39319000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
34	chr19:39315400-39319800	Genic enhancers	Fetal Intestine Small	intestine
35	chr19:39315600-39321000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:39315800-39318200	Weak transcription	Fetal Brain Male	brain
37	chr19:39316000-39321400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:39316000-39321600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:39316200-39318200	Enhancers	Fetal Heart	heart
40	chr19:39316200-39319600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:39316200-39320600	Strong transcription	Brain Germinal Matrix	brain
42	chr19:39316200-39321400	Genic enhancers	Placenta	Placenta
43	chr19:39316400-39318400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
44	chr19:39316400-39318800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr19:39316400-39319000	Genic enhancers	Liver	Liver
46	chr19:39316400-39319000	Genic enhancers	Left Ventricle	heart
47	chr19:39316400-39319200	Strong transcription	Brain Anterior Caudate	brain
48	chr19:39316400-39319600	Strong transcription	Primary T cells from cord blood	blood
49	chr19:39316400-39320600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr19:39316600-39318600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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