Variant report

Variant	rs13147824
Chromosome Location	chr4:57297996-57297997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57278722..57280888-chr4:57296778..57299271,2	MCF-7	breast:
2	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
3	chr4:57297760..57299581-chr4:57396785..57398752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000270109	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10015221	0.90[JPT][hapmap]
rs10015634	0.89[JPT][hapmap]
rs10031012	0.81[EUR][1000 genomes]
rs10031550	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10518	0.89[JPT][hapmap]
rs10866433	0.90[JPT][hapmap]
rs11133439	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs11724302	0.88[CEU][hapmap]
rs11733474	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12331363	0.82[ASN][1000 genomes]
rs12331412	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13114104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133016	0.88[EUR][1000 genomes]
rs13141793	0.95[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1356788	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1401907	0.87[CEU][hapmap]
rs1401912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1464286	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474178	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17051687	0.89[JPT][hapmap]
rs17086803	0.90[JPT][hapmap]
rs1976815	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996650	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2030365	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2049087	0.94[JPT][hapmap]
rs2139512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292985	0.87[CEU][hapmap]
rs28559894	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2899063	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796542	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796547	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs3822003	0.86[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4073691	0.94[JPT][hapmap]
rs4167	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4305581	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs4865087	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865090	0.86[CEU][hapmap]
rs4865100	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865101	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57503982	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59615456	0.80[EUR][1000 genomes]
rs62310633	0.82[EUR][1000 genomes]
rs6554345	0.80[CEU][hapmap]
rs6554348	0.87[CEU][hapmap]
rs6554349	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6554352	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554355	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554356	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811821	0.89[JPT][hapmap]
rs6812041	0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819534	0.94[JPT][hapmap]
rs6826795	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6834736	0.81[YRI][hapmap]
rs6841016	0.86[EUR][1000 genomes]
rs7657711	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7661712	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7683781	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7692385	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7693137	0.87[CEU][hapmap]
rs7693683	0.91[EUR][1000 genomes]
rs7700034	0.84[JPT][hapmap]
rs9683679	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9684298	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9993277	0.82[CEU][hapmap]
rs9996593	0.94[JPT][hapmap]
rs9997639	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13147824	PPAT	cis	normal skin	skin_eQTL
rs13147824	PPAT	cis	uninvolved skin	skin_eQTL
rs13147824	PPAT	cis	lesional skin	skin_eQTL
rs13147824	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
4	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
5	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:57277000-57300000	Weak transcription	HSMM	muscle
8	chr4:57277800-57298000	Weak transcription	A549	lung
9	chr4:57278000-57299200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:57278200-57300200	Weak transcription	Fetal Kidney	kidney
11	chr4:57278200-57300200	Weak transcription	NHDF-Ad	bronchial
12	chr4:57280800-57299400	Weak transcription	Fetal Lung	lung
13	chr4:57281000-57299200	Weak transcription	HMEC	breast
14	chr4:57284800-57300400	Weak transcription	Fetal Intestine Small	intestine
15	chr4:57287800-57299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:57288000-57299200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:57289600-57299800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:57292000-57299200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:57292200-57298000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:57292200-57299200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:57292200-57299200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:57292200-57299200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:57292200-57299800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:57292400-57298000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:57293400-57298800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:57293400-57299200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:57294000-57299200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:57295000-57299200	Enhancers	HepG2	liver
29	chr4:57295000-57305000	Active TSS	GM12878-XiMat	blood
30	chr4:57295400-57300000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:57296400-57299400	Weak transcription	HUVEC	blood vessel
32	chr4:57296600-57298600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:57296600-57300400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:57297200-57300000	Weak transcription	Fetal Brain Male	brain
35	chr4:57297400-57298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:57297400-57298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:57297600-57298000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:57297600-57298200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:57297600-57298200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr4:57297600-57298400	Enhancers	Brain Germinal Matrix	brain
41	chr4:57297800-57298200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:57297800-57298200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:57297800-57298200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:57297800-57298200	Flanking Active TSS	Dnd41	blood
45	chr4:57297800-57298200	Transcr. at gene 5' and 3'	K562	blood
46	chr4:57297800-57298400	Flanking Active TSS	Hela-S3	cervix

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