Variant report

Variant	rs55955981
Chromosome Location	chr19:36281949-36281950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36272002..36276478-chr19:36278525..36283309,6	K562	blood:
2	chr19:36184725..36185454-chr19:36281716..36282604,3	K562	blood:
3	chr19:36276618..36278741-chr19:36279963..36282089,2	K562	blood:
4	chr19:36273554..36275666-chr19:36279715..36282125,2	MCF-7	breast:
5	chr19:36281922..36284549-chr19:36300650..36302438,2	K562	blood:
6	chr19:36257583..36262889-chr19:36280442..36283468,4	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRODH2-1	chr19:36281919-36282754	ENSG00000225872
2	lnc-PRODH2-1	chr19:36281919-36282754	NR_104176

No data

Variant related genes	Relation type
ENSG00000267049	Chromatin interaction
ENSG00000167595	Chromatin interaction
ENSG00000004777	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11546662	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11546665	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11881242	0.94[EUR][1000 genomes]
rs34562867	0.82[EUR][1000 genomes]
rs35297478	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3817622	0.83[EUR][1000 genomes]
rs3893069	0.83[EUR][1000 genomes]
rs4992668	0.83[EUR][1000 genomes]
rs56237993	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56813196	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58255615	0.83[EUR][1000 genomes]
rs73590591	0.82[EUR][1000 genomes]
rs73590598	0.83[EUR][1000 genomes]
rs73592416	0.83[EUR][1000 genomes]
rs73592448	0.92[EUR][1000 genomes]
rs73592461	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs73592484	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73594410	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
6	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
7	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
8	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
9	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv911637	chr19:36261928-36309321	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36267800-36284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr19:36268400-36284200	Weak transcription	K562	blood
3	chr19:36273000-36282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:36273200-36284200	Weak transcription	Osteobl	bone
5	chr19:36273600-36283400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:36273600-36288000	Weak transcription	Brain Angular Gyrus	brain
7	chr19:36273800-36284000	Weak transcription	Esophagus	oesophagus
8	chr19:36274000-36284000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:36274200-36282600	Weak transcription	Fetal Lung	lung
10	chr19:36274200-36284000	Weak transcription	Brain Anterior Caudate	brain
11	chr19:36274600-36284000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr19:36277000-36282200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:36277200-36284400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:36277400-36288200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:36277600-36284800	Weak transcription	Gastric	stomach
16	chr19:36277800-36283200	Weak transcription	Fetal Thymus	thymus
17	chr19:36278000-36282400	Weak transcription	Fetal Intestine Small	intestine
18	chr19:36278400-36282000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:36278400-36282600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:36278400-36288000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:36278400-36294400	Weak transcription	Spleen	Spleen
22	chr19:36278600-36284000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:36278600-36284200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr19:36278600-36284200	Weak transcription	NHLF	lung
25	chr19:36278600-36284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:36278800-36282000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:36278800-36282000	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:36278800-36282600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:36279000-36285000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:36279200-36284800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:36279200-36285000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:36279400-36285800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:36279600-36282400	Weak transcription	Thymus	Thymus
34	chr19:36280000-36282200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr19:36280800-36282200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:36281000-36282200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:36281000-36285600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:36281200-36287200	Weak transcription	Fetal Brain Female	brain
39	chr19:36281200-36287600	Weak transcription	Brain Germinal Matrix	brain
40	chr19:36281800-36282000	Enhancers	Fetal Muscle Leg	muscle
41	chr19:36281800-36282200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:36281800-36282400	Flanking Active TSS	HepG2	liver
43	chr19:36281800-36283400	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links