Variant report

Variant	rs28612323
Chromosome Location	chr19:40011564-40011565
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39993528..39996626-chr19:40010694..40012599,3	K562	blood:
2	chr19:40010850..40013906-chr19:40015655..40017773,3	K562	blood:
3	chr19:40009365..40013772-chr19:40013811..40019532,6	K562	blood:
4	chr19:40008253..40012743-chr19:40028297..40031526,4	MCF-7	breast:
5	chr19:40009271..40012163-chr19:40025249..40026752,2	K562	blood:
6	chr19:39996434..39999971-chr19:40007133..40012367,8	K562	blood:
7	chr19:39987449..39990111-chr19:40010646..40012168,2	K562	blood:
8	chr19:39939856..39941421-chr19:40009261..40011843,2	K562	blood:
9	chr19:40005114..40007099-chr19:40009301..40012278,2	K562	blood:
10	chr19:40009851..40011613-chr19:40024915..40027349,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269584	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000186838	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	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10404127	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418049	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28411237	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28596775	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];0.85[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
rs28612323	PNMAL1	cis	cerebellum	SCAN
rs28612323	RABAC1	cis	cerebellum	SCAN
rs28612323	EID2B	cis	lymphoblastoid	seeQTL
rs28612323	DHX34	cis	cerebellum	SCAN
rs28612323	PVRL2	cis	cerebellum	SCAN
rs28612323	CIC	cis	parietal	SCAN
rs28612323	TPRX1	cis	cerebellum	SCAN
rs28612323	B3GNT8	cis	parietal	SCAN

Chromatin state (count:35 , 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	chr19:40007200-40018200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:40008000-40022200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:40009400-40021200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr19:40009600-40011600	Weak transcription	HepG2	liver
8	chr19:40009800-40022200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:40009800-40022400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:40009800-40022600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:40009800-40022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:40010000-40011600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr19:40010000-40015200	Weak transcription	Fetal Stomach	stomach
14	chr19:40010000-40016000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:40010000-40019000	Weak transcription	A549	lung
16	chr19:40010000-40022200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr19:40010000-40022200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:40010000-40022600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr19:40010000-40022600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:40010200-40022400	Weak transcription	Fetal Muscle Leg	muscle
21	chr19:40010600-40011600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:40010600-40015800	Weak transcription	Fetal Brain Female	brain
23	chr19:40010800-40013000	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr19:40011000-40012400	Enhancers	K562	blood
25	chr19:40011000-40015200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:40011000-40022000	Weak transcription	Fetal Thymus	thymus
27	chr19:40011200-40012600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr19:40011200-40012600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:40011200-40012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:40011200-40021200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:40011200-40022200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:40011200-40022400	Weak transcription	Fetal Kidney	kidney
33	chr19:40011400-40011600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:40011400-40012400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:40011400-40020600	Weak transcription	Brain Inferior Temporal Lobe	brain

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