Variant report

Variant	rs3814872
Chromosome Location	chr14:71227913-71227914
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71225781..71229364-chr14:71273423..71276710,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10129307	0.81[CEU][hapmap]
rs1034769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873241	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873242	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12589737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879569	0.87[ASW][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap]
rs1476609	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1476610	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes]
rs2023955	0.91[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap]
rs2107665	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2107666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2332455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2332458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4141095	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes]
rs4899367	0.81[MKK][hapmap]
rs4899368	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[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];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4899369	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902844	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4902852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[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]
rs4902863	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs6573978	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes]
rs6573980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7152516	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7155910	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs8006424	0.81[MKK][hapmap]
rs8007131	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8011047	0.86[GIH][hapmap]
rs8011507	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8018294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3814872	FAM71D	cis	cerebellum	SCAN
rs3814872	DPF3	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71197000-71228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr14:71201200-71228000	Weak transcription	Colonic Mucosa	Colon
3	chr14:71204800-71229400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr14:71206800-71231600	Weak transcription	Brain Anterior Caudate	brain
5	chr14:71209200-71229400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr14:71209400-71238200	Weak transcription	Fetal Stomach	stomach
7	chr14:71209400-71238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr14:71209400-71238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr14:71209600-71229000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr14:71212000-71238200	Weak transcription	Fetal Intestine Small	intestine
11	chr14:71215800-71232200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr14:71216400-71238200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:71216600-71245800	Weak transcription	Brain Germinal Matrix	brain
14	chr14:71216800-71238400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:71220200-71229000	Weak transcription	Brain Angular Gyrus	brain
16	chr14:71220600-71231400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr14:71220600-71238600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:71220800-71240400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr14:71220800-71266400	Weak transcription	Fetal Intestine Large	intestine
20	chr14:71221000-71237600	Weak transcription	Fetal Kidney	kidney
21	chr14:71221800-71239600	Weak transcription	Liver	Liver
22	chr14:71222200-71238000	Weak transcription	Esophagus	oesophagus
23	chr14:71222200-71238200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr14:71222200-71238200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr14:71222200-71258200	Weak transcription	HepG2	liver
26	chr14:71222400-71230400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr14:71222400-71238200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr14:71222600-71229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
30	chr14:71222800-71238200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr14:71223000-71258400	Weak transcription	Primary T cells from cord blood	blood
32	chr14:71223000-71266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:71223400-71240000	Weak transcription	Pancreas	Pancrea
34	chr14:71223600-71229000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr14:71223600-71230600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr14:71223600-71232200	Weak transcription	Primary B cells from cord blood	blood
37	chr14:71224000-71228800	Strong transcription	HMEC	breast
38	chr14:71224000-71258000	Weak transcription	Dnd41	blood
39	chr14:71225600-71228000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr14:71225800-71229000	Strong transcription	NHEK	skin
41	chr14:71226200-71228000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr14:71226200-71228000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr14:71226200-71228200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr14:71226400-71228000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr14:71226400-71228000	Strong transcription	A549	lung
46	chr14:71226800-71228000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr14:71226800-71228000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr14:71226800-71228200	Strong transcription	Fetal Brain Female	brain
49	chr14:71227000-71228000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr14:71227000-71228000	Strong transcription	Pancreatic Islets	Pancreatic Islet

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