Variant report

Variant	rs8112499
Chromosome Location	chr19:38868131-38868132
allele	C/T
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	chr19:38867803-38868187	K562	blood:	n/a	n/a
2	POLR2A	chr19:38868106-38868351	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:38868016-38868270	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
2	chr19:38793026..38794538-chr19:38866336..38868984,2	K562	blood:

Variant related genes	Relation type
PSMD8	TF binding region
ENSG00000266963	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10993	1.00[CEU][hapmap]
rs11083454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11538289	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880301	1.00[CEU][hapmap]
rs2302228	1.00[EUR][1000 genomes]
rs3745955	0.80[EUR][1000 genomes]
rs3745963	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745964	1.00[CEU][hapmap]
rs3760884	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57753437	0.93[EUR][1000 genomes]
rs59491640	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60780508	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508791	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248540	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248780	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257976	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043029	0.81[EUR][1000 genomes]
rs73043030	0.93[EUR][1000 genomes]
rs73043033	0.93[EUR][1000 genomes]
rs73043098	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73044905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044908	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044923	0.80[EUR][1000 genomes]
rs73044926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044930	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044932	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8108440	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109713	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38866400-38869800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38866400-38870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:38866400-38876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:38866600-38868200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:38866600-38869600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr19:38866800-38868200	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr19:38866800-38868400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:38866800-38869600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:38866800-38869800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:38866800-38869800	Weak transcription	Fetal Kidney	kidney
11	chr19:38866800-38871600	Weak transcription	Small Intestine	intestine
12	chr19:38867000-38868400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:38867000-38869600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:38867000-38874600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:38867000-38874800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:38867000-38874800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr19:38867000-38875600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:38867000-38877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:38867000-38878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:38867200-38868600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:38867200-38869400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:38867200-38871600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:38867200-38872000	Weak transcription	Stomach Mucosa	stomach
24	chr19:38867200-38874600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr19:38867200-38874800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:38867200-38874800	Strong transcription	Fetal Intestine Large	intestine
27	chr19:38867200-38875200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr19:38867200-38875400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:38867200-38877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:38867200-38877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr19:38867200-38877400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:38867400-38868200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:38867400-38868600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:38867400-38869800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:38867400-38869800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr19:38867400-38869800	Weak transcription	Brain Substantia Nigra	brain
37	chr19:38867400-38871800	Weak transcription	Fetal Brain Male	brain
38	chr19:38867400-38874400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:38867400-38875000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr19:38867400-38875800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr19:38867600-38868200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr19:38867600-38868200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:38867600-38868600	Weak transcription	Ovary	ovary
44	chr19:38867600-38868800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
45	chr19:38867600-38869000	Strong transcription	Osteobl	bone
46	chr19:38867600-38869600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:38867600-38869600	Weak transcription	Fetal Lung	lung
48	chr19:38867600-38869600	Weak transcription	Fetal Thymus	thymus
49	chr19:38867600-38869600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:38867600-38869800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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