Variant report

Variant	rs3809425
Chromosome Location	chr14:96986153-96986154
allele	A/G
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	chr14:96985888-96986287	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:96966203..96970615-chr14:96984362..96986675,5	MCF-7	breast:
2	chr14:96985630..96987652-chr14:97013134..97015914,2	MCF-7	breast:
3	chr14:96984347..96986683-chr14:97013576..97015718,2	K562	blood:

Variant related genes	Relation type
PAPOLA	TF binding region
ENSG00000260806	Chromatin interaction
ENSG00000090060	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10136266	0.83[JPT][hapmap]
rs10143834	0.83[JPT][hapmap]
rs10145194	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1038439	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs11160341	0.83[JPT][hapmap]
rs11160343	0.81[ASN][1000 genomes]
rs11621566	0.83[GIH][hapmap];0.83[JPT][hapmap]
rs11623142	0.83[JPT][hapmap]
rs12147170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12147717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12586332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12586789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12589747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329034	0.83[JPT][hapmap]
rs13379390	0.83[JPT][hapmap]
rs1484251	0.82[JPT][hapmap]
rs17094149	0.82[JPT][hapmap]
rs2274795	0.83[JPT][hapmap]
rs2297243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28405063	0.88[ASN][1000 genomes]
rs28600893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28686887	0.86[ASN][1000 genomes]
rs28718054	0.83[JPT][hapmap]
rs56088908	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56254662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59323239	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61368673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7142226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7142806	0.83[JPT][hapmap]
rs7160148	0.83[JPT][hapmap]
rs72706848	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72706852	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72706853	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72706857	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72706860	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72706863	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72706864	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8003976	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8013517	0.83[JPT][hapmap]

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	nsv1042409	chr14:96832303-97115668	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv542178	chr14:96832303-97115668	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv902211	chr14:96864309-96986153	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	esv3442210	chr14:96878392-97038700	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv1802671	chr14:96942352-97035680	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1052499	chr14:96974524-97034805	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv1793036	chr14:96983291-97023059	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:96970000-96987000	Enhancers	Primary B cells from peripheral blood	blood
2	chr14:96970600-96987800	Weak transcription	Fetal Stomach	stomach
3	chr14:96970600-96990600	Weak transcription	NH-A	brain
4	chr14:96970600-96991200	Weak transcription	Fetal Kidney	kidney
5	chr14:96970800-96987400	Weak transcription	HSMM	muscle
6	chr14:96970800-96988400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:96971200-96987400	Weak transcription	Osteobl	bone
8	chr14:96971600-96989800	Weak transcription	NHLF	lung
9	chr14:96971800-96990800	Weak transcription	HMEC	breast
10	chr14:96971800-96991000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr14:96972200-96986400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr14:96972200-96986600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:96972200-96987800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:96972200-96988200	Weak transcription	Colonic Mucosa	Colon
15	chr14:96972400-96986200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:96972400-96986600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr14:96972400-96987800	Weak transcription	Esophagus	oesophagus
18	chr14:96972400-96987800	Weak transcription	Spleen	Spleen
19	chr14:96973400-96986600	Weak transcription	Fetal Thymus	thymus
20	chr14:96974600-96987800	Weak transcription	Gastric	stomach
21	chr14:96974600-96987800	Weak transcription	Lung	lung
22	chr14:96975000-96992400	Weak transcription	K562	blood
23	chr14:96975400-96989200	Weak transcription	Hela-S3	cervix
24	chr14:96975600-96986400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr14:96975600-96987800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr14:96975600-96992200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:96976000-96987200	Weak transcription	NHDF-Ad	bronchial
28	chr14:96976200-96988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr14:96976200-96992400	Weak transcription	NHEK	skin
30	chr14:96977000-96992600	Weak transcription	Fetal Brain Male	brain
31	chr14:96977600-96987800	Weak transcription	Dnd41	blood
32	chr14:96977600-96988000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr14:96977800-96986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr14:96978000-97019400	Weak transcription	Aorta	Aorta
35	chr14:96979200-96986800	Enhancers	Primary B cells from cord blood	blood
36	chr14:96979400-96987800	Weak transcription	Brain Germinal Matrix	brain
37	chr14:96979400-96988000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr14:96979400-96988800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:96979600-96986400	Weak transcription	Fetal Intestine Large	intestine
40	chr14:96979600-96986800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr14:96979600-96987400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr14:96979600-96987800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr14:96979600-96987800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr14:96979600-96987800	Weak transcription	Thymus	Thymus
45	chr14:96979600-97000200	Weak transcription	Fetal Heart	heart
46	chr14:96979600-97022400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr14:96979800-96987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr14:96979800-96987800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr14:96979800-96987800	Weak transcription	Pancreas	Pancrea
50	chr14:96979800-97019200	Weak transcription	Small Intestine	intestine

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