Variant report

Variant	rs28596775
Chromosome Location	chr19:40009466-40009467
allele	G/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40009365..40013772-chr19:40013811..40019532,6	K562	blood:
2	chr19:40004361..40006342-chr19:40008236..40011179,2	K562	blood:
3	chr19:40008391..40010217-chr19:40029919..40032075,2	K562	blood:
4	chr19:40008327..40011213-chr19:40021450..40023103,2	K562	blood:
5	chr19:40008253..40012743-chr19:40028297..40031526,4	MCF-7	breast:
6	chr19:40007684..40010217-chr19:40028799..40031419,2	K562	blood:
7	chr19:40009271..40012163-chr19:40025249..40026752,2	K562	blood:
8	chr19:40008044..40009620-chr19:40022732..40025269,2	MCF-7	breast:
9	chr19:39996434..39999971-chr19:40007133..40012367,8	K562	blood:
10	chr19:39939856..39941421-chr19:40009261..40011843,2	K562	blood:
11	chr19:40005114..40007099-chr19:40009301..40012278,2	K562	blood:
12	chr19:39970685..39973008-chr19:40008116..40011031,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269584	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000186838	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10403763	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10404127	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10418049	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28411237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28612323	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101913	0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	esv3374976	chr19:39998161-40023263	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv960762	chr19:40006922-40023016	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs28596775	TPRX1	cis	cerebellum	SCAN
rs28596775	DHX34	cis	cerebellum	SCAN
rs28596775	PVRL2	cis	cerebellum	SCAN
rs28596775	B3GNT8	cis	parietal	SCAN
rs28596775	RABAC1	cis	cerebellum	SCAN
rs28596775	CIC	cis	parietal	SCAN
rs28596775	PNMAL1	cis	cerebellum	SCAN
rs28596775	EID2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40006600-40022800	Weak transcription	Lung	lung
2	chr19:40006800-40015200	Weak transcription	Right Atrium	heart
3	chr19:40007000-40022400	Weak transcription	Right Ventricle	heart
4	chr19:40007200-40010000	Weak transcription	Fetal Kidney	kidney
5	chr19:40007200-40010200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:40007200-40018200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:40008000-40022200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:40008400-40009600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:40009000-40009800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:40009000-40009800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:40009000-40010000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:40009000-40010000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:40009000-40010000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:40009000-40010000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:40009000-40010200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr19:40009200-40009800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr19:40009200-40009800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr19:40009200-40010000	Enhancers	A549	lung
19	chr19:40009200-40010000	Flanking Active TSS	K562	blood
20	chr19:40009200-40010800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:40009200-40011400	Enhancers	Placenta	Placenta
22	chr19:40009400-40009600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:40009400-40009600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:40009400-40009600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:40009400-40009800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
26	chr19:40009400-40009800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr19:40009400-40009800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr19:40009400-40009800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:40009400-40009800	Flanking Bivalent TSS/Enh	NHEK	skin
30	chr19:40009400-40010000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:40009400-40010000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr19:40009400-40021200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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