Variant report

Variant	rs231241
Chromosome Location	chr19:36245413-36245414
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	chr19:36243424-36249712	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36245255..36250047-chr19:36263979..36267864,8	K562	blood:

Variant related genes	Relation type
C19orf55	TF binding region
ENSG00000267328	TF binding region
ENSG00000267439	TF binding region
ENSG00000004777	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10419971	0.81[GIH][hapmap]
rs11878987	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881839	0.81[GIH][hapmap]
rs16970648	0.83[CEU][hapmap];0.88[GIH][hapmap];0.90[EUR][1000 genomes]
rs34485834	1.00[EUR][1000 genomes]
rs34632325	1.00[EUR][1000 genomes]
rs35843967	1.00[EUR][1000 genomes]
rs7252936	0.81[EUR][1000 genomes]
rs7254581	0.91[CEU][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7256373	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs231241	F25965	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36240000-36246200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:36240200-36246200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:36240400-36246200	Weak transcription	NH-A	brain
4	chr19:36240400-36246400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:36240400-36247200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:36241000-36245600	Weak transcription	Fetal Heart	heart
7	chr19:36241000-36245800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:36241000-36245800	Strong transcription	Fetal Intestine Small	intestine
9	chr19:36241000-36246000	Weak transcription	Small Intestine	intestine
10	chr19:36241000-36246200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr19:36241000-36246200	Weak transcription	HUVEC	blood vessel
12	chr19:36241000-36247600	Weak transcription	HMEC	breast
13	chr19:36241200-36245800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:36241200-36247800	Weak transcription	Hela-S3	cervix
15	chr19:36241800-36245800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:36242000-36245600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:36242200-36245800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:36242200-36246400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:36242400-36245600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:36242400-36245600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr19:36242400-36245600	Strong transcription	Fetal Intestine Large	intestine
22	chr19:36242400-36245600	Strong transcription	Osteobl	bone
23	chr19:36242400-36246000	Strong transcription	NHLF	lung
24	chr19:36242400-36247200	Strong transcription	A549	lung
25	chr19:36242600-36245600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr19:36242600-36245600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:36242600-36245600	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr19:36242600-36245600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:36242600-36245600	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr19:36242600-36247000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:36242600-36247200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:36242800-36245600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:36242800-36245600	Strong transcription	Liver	Liver
34	chr19:36242800-36245600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:36242800-36245800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:36242800-36246000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:36242800-36246000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:36242800-36246000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr19:36242800-36246200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:36242800-36246200	Strong transcription	Brain Germinal Matrix	brain
41	chr19:36242800-36246400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:36243000-36245600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:36243000-36245600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:36243000-36245600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr19:36243000-36245600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:36243000-36245600	Strong transcription	Brain Anterior Caudate	brain
47	chr19:36243000-36245600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr19:36243000-36245600	Strong transcription	HepG2	liver
49	chr19:36243000-36245800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:36243000-36245800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links