Variant report

Variant	rs3786950
Chromosome Location	chr19:39988164-39988165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr19:39988020-39991615	PANC-1	pancreas:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39925200..39927476-chr19:39987141..39989306,2	K562	blood:
2	chr19:39986104..39989101-chr19:39992054..39994014,2	K562	blood:
3	chr19:39970388..39973416-chr19:39987093..39991960,6	MCF-7	breast:
4	chr19:39987217..39989716-chr19:40005337..40006880,2	MCF-7	breast:
5	chr19:39982701..39986911-chr19:39987055..39990908,4	MCF-7	breast:
6	chr19:39973981..39976601-chr19:39986100..39988186,2	MCF-7	breast:
7	chr19:39987898..39989106-chr19:40023124..40024390,5	MCF-7	breast:
8	chr19:39925162..39927908-chr19:39986730..39988641,3	K562	blood:
9	chr19:39978061..39981122-chr19:39987269..39990771,3	MCF-7	breast:
10	chr19:39831059..39833135-chr19:39987962..39989581,2	MCF-7	breast:
11	chr19:39987415..39989103-chr19:40024922..40026576,2	MCF-7	breast:

No data

Variant related genes	Relation type
DLL3	TF binding region
ENSG00000105193	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000186838	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10425652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10426543	0.80[CHB][hapmap]
rs11882744	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs1529733	0.86[CHB][hapmap]
rs1865093	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs4802030	0.86[CHB][hapmap]
rs4802032	1.00[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs4802033	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803248	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62120691	0.82[ASN][1000 genomes]
rs8106642	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3786950	RPS16	cis	Lymphoblastoid	GTEx
rs3786950	RPS16	cis	Heart Left Ventricle	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
2	chr19:39973600-39988400	Weak transcription	Fetal Brain Male	brain
3	chr19:39980000-39988600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr19:39980600-39988600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:39980800-39988200	Weak transcription	HUVEC	blood vessel
6	chr19:39980800-39988400	Weak transcription	K562	blood
7	chr19:39981000-39988200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:39981000-39988400	Weak transcription	Aorta	Aorta
9	chr19:39981000-39988400	Weak transcription	GM12878-XiMat	blood
10	chr19:39981000-39988400	Weak transcription	HSMMtube	muscle
11	chr19:39981000-39988600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:39981000-39988600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:39981000-39988600	Weak transcription	Gastric	stomach
14	chr19:39981000-39988800	Weak transcription	Pancreas	Pancrea
15	chr19:39981200-39988400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr19:39981400-39988200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr19:39981400-39988400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:39981400-39988600	Weak transcription	Primary B cells from cord blood	blood
19	chr19:39981400-39988600	Weak transcription	HSMM	muscle
20	chr19:39981600-39988400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:39983200-39988400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:39983200-39988400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:39983200-39988400	Weak transcription	Fetal Brain Female	brain
24	chr19:39983200-39988400	Weak transcription	Spleen	Spleen
25	chr19:39983200-39988600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:39983200-39988800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:39983400-39988200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:39983800-39988200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:39983800-39988200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:39984000-39988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:39984000-39988200	Weak transcription	A549	lung
32	chr19:39984000-39988600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:39984200-39988600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:39987200-39988200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr19:39987600-39988400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr19:39987600-39988400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:39988000-39988200	Active TSS	Brain Germinal Matrix	brain
38	chr19:39988000-39988800	Bivalent Enhancer	Fetal Stomach	stomach

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