Variant report

Variant	rs162117
Chromosome Location	chr19:52870815-52870816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs162126	0.84[EUR][1000 genomes]
rs162127	0.90[EUR][1000 genomes]
rs182751	0.93[EUR][1000 genomes]
rs2657916	0.83[EUR][1000 genomes]
rs324121	0.90[EUR][1000 genomes]
rs324122	0.82[EUR][1000 genomes]
rs324124	0.90[EUR][1000 genomes]
rs324125	0.90[EUR][1000 genomes]
rs707311	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73581131	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs810592	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs162117	LOC400713	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52858800-52871800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:52861800-52872200	ZNF genes & repeats	Fetal Lung	lung
4	chr19:52862000-52871000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr19:52862000-52871000	ZNF genes & repeats	Fetal Brain Female	brain
6	chr19:52862000-52871200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:52862600-52871400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:52865200-52871200	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:52865600-52871200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:52866000-52871200	ZNF genes & repeats	Dnd41	blood
12	chr19:52866600-52872200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
14	chr19:52866800-52871200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr19:52866800-52871200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:52867200-52872400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
17	chr19:52867600-52871000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
18	chr19:52867600-52871200	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr19:52867600-52872200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
20	chr19:52867800-52871400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:52867800-52872200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:52868200-52871200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:52868200-52871200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr19:52868400-52871200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr19:52868600-52871000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:52868600-52871000	ZNF genes & repeats	HSMMtube	muscle
27	chr19:52869800-52872600	Weak transcription	Fetal Kidney	kidney
28	chr19:52869800-52872800	Weak transcription	Gastric	stomach
29	chr19:52870000-52872800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:52870000-52872800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:52870000-52872800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:52870000-52872800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:52870000-52872800	Weak transcription	Aorta	Aorta
34	chr19:52870000-52872800	Weak transcription	Fetal Brain Male	brain
35	chr19:52870000-52872800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr19:52870200-52872800	Weak transcription	Brain Angular Gyrus	brain
37	chr19:52870200-52872800	Weak transcription	Brain Anterior Caudate	brain
38	chr19:52870200-52872800	Weak transcription	Brain Substantia Nigra	brain
39	chr19:52870200-52872800	Weak transcription	Ovary	ovary
40	chr19:52870800-52871000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:52870800-52871000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
42	chr19:52870800-52871000	ZNF genes & repeats	Colon Smooth Muscle	Colon
43	chr19:52870800-52872000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links