Variant report

Variant	rs4919967
Chromosome Location	chr21:44599812-44599813
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44595907..44598227-chr21:44599190..44600855,2	MCF-7	breast:
2	chr21:44595975..44600241-chr21:44843202..44849395,11	MCF-7	breast:
3	chr21:44596302..44600320-chr21:44763162..44765941,4	MCF-7	breast:
4	chr21:44596910..44599943-chr21:44921245..44924609,4	MCF-7	breast:
5	chr21:44590676..44595436-chr21:44598084..44601687,4	K562	blood:
6	chr21:44599423..44602035-chr21:44607332..44609772,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11203177	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11702241	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs11909053	0.86[AMR][1000 genomes]
rs11909888	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11910132	0.82[ASW][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11910213	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2839641	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839642	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2839643	0.92[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2839647	0.81[AMR][1000 genomes]
rs2839648	0.86[AMR][1000 genomes]
rs2839649	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28970980	0.80[ASN][1000 genomes]
rs28971677	0.80[ASN][1000 genomes]
rs4919966	0.93[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7276342	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7280964	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913812	chr21:44213057-44686358	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1067412	chr21:44526656-44772130	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1060276	chr21:44550394-44628579	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv913832	chr21:44579105-44768562	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv3440728	chr21:44595883-44600181	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	esv3427846	chr21:44597783-44602181	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv3430571	chr21:44598283-44602181	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv3369197	chr21:44598383-44602181	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4919967	PDE9A	cis	parietal	SCAN
rs4919967	TMPRSS3	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44593800-44601600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:44595600-44602400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr21:44596400-44600400	Enhancers	Spleen	Spleen
4	chr21:44596600-44600800	Enhancers	Pancreas	Pancrea
5	chr21:44596600-44601600	Enhancers	HMEC	breast
6	chr21:44596800-44602400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr21:44597000-44600000	Enhancers	Lung	lung
8	chr21:44597000-44601800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr21:44597200-44601400	Enhancers	Brain Germinal Matrix	brain
10	chr21:44597400-44600200	Enhancers	Right Ventricle	heart
11	chr21:44597600-44601400	Enhancers	Fetal Brain Female	brain
12	chr21:44597600-44601600	Enhancers	Esophagus	oesophagus
13	chr21:44597800-44600000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr21:44597800-44601400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr21:44598000-44600600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr21:44598000-44600800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr21:44598200-44600000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr21:44598200-44600400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr21:44598200-44600400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr21:44598200-44600400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr21:44598200-44600400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr21:44598200-44601000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr21:44598200-44601600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr21:44598400-44600000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr21:44598400-44600200	Enhancers	Duodenum Mucosa	Duodenum
26	chr21:44598400-44600800	Enhancers	Fetal Heart	heart
27	chr21:44598400-44602800	Weak transcription	Brain Hippocampus Middle	brain
28	chr21:44598800-44601600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr21:44599000-44601200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr21:44599200-44603000	Weak transcription	Colonic Mucosa	Colon
31	chr21:44599200-44614200	Weak transcription	Right Atrium	heart
32	chr21:44599400-44600200	Flanking Active TSS	Fetal Lung	lung
33	chr21:44599400-44601200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr21:44599600-44600000	Weak transcription	Primary T cells from cord blood	blood
35	chr21:44599800-44600000	Enhancers	Gastric	stomach
36	chr21:44599800-44600200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr21:44599800-44600200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
38	chr21:44599800-44600200	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
39	chr21:44599800-44600200	ZNF genes & repeats	NHEK	skin
40	chr21:44599800-44600600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr21:44599800-44601000	Weak transcription	Placenta	Placenta

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