Variant report

Variant	rs10415077
Chromosome Location	chr19:39930081-39930082
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	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39930044..39931944-chr19:39980921..39983797,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213922	TF binding region
RPS16	TF binding region
SUPT5H	TF binding region
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10408589	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409917	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10410092	0.96[AFR][1000 genomes]
rs10413140	1.00[EUR][1000 genomes]
rs10413673	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415279	1.00[EUR][1000 genomes]
rs10425566	1.00[YRI][hapmap]
rs10425873	0.81[AFR][1000 genomes]
rs13346052	1.00[EUR][1000 genomes]
rs2230765	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4100178	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39926600-39935200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:39927400-39930200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39927400-39930400	Weak transcription	K562	blood
4	chr19:39927400-39930800	Weak transcription	Brain Angular Gyrus	brain
5	chr19:39927400-39935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:39927400-39935200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:39927400-39935200	Weak transcription	Gastric	stomach
8	chr19:39927400-39935200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:39927600-39930200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:39927600-39930200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:39927600-39930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:39927600-39930600	Weak transcription	GM12878-XiMat	blood
13	chr19:39927600-39930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:39927600-39930800	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:39927600-39930800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr19:39927600-39930800	Weak transcription	Fetal Heart	heart
17	chr19:39927600-39931000	Weak transcription	Primary B cells from cord blood	blood
18	chr19:39927600-39931000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr19:39927600-39931000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:39927600-39931000	Weak transcription	Liver	Liver
21	chr19:39927600-39931000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:39927600-39931000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr19:39927600-39932000	Enhancers	A549	lung
24	chr19:39927600-39934800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:39927600-39935000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:39927600-39935000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:39927600-39935000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:39927600-39935000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:39927600-39935000	Weak transcription	HMEC	breast
30	chr19:39927600-39935200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:39927600-39935200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:39927600-39935200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:39927600-39935200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:39927600-39935200	Weak transcription	Brain Anterior Caudate	brain
35	chr19:39927600-39935200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:39927600-39935200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr19:39927600-39935200	Weak transcription	Fetal Kidney	kidney
38	chr19:39927600-39935200	Weak transcription	HSMMtube	muscle
39	chr19:39927600-39935200	Weak transcription	NHLF	lung
40	chr19:39927800-39931000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:39927800-39931000	Weak transcription	Dnd41	blood
42	chr19:39927800-39931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:39928600-39930800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr19:39928600-39935000	Weak transcription	Fetal Intestine Small	intestine
45	chr19:39928800-39930600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:39929000-39930800	Weak transcription	Hela-S3	cervix
47	chr19:39929200-39930200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:39929200-39932000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:39929200-39932200	Enhancers	HepG2	liver
50	chr19:39929400-39931200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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