Variant report

Variant	rs11728110
Chromosome Location	chr4:57293077-57293078
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57290938..57296949-chr4:57297532..57303755,13	MCF-7	breast:
2	chr4:57291412..57293636-chr4:57775068..57776675,2	K562	blood:
3	chr4:57288977..57293143-chr4:57294508..57297491,5	K562	blood:
4	chr4:57266768..57270858-chr4:57291904..57297499,5	K562	blood:
5	chr4:57275029..57278238-chr4:57292178..57294755,3	K562	blood:

Variant related genes	Relation type
ENSG00000128050	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000268171	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11930159	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13102012	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13102298	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13124696	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13134963	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13135046	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13147132	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13150159	0.83[EUR][1000 genomes]
rs2030364	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554347	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6854758	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7694439	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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	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
5	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11728110	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs11728110	AASDH	cis	Skin Sun Exposed Lower leg	GTEx
rs11728110	AASDH	cis	lung	GTEx
rs11728110	AASDH	cis	multi-tissue	Pritchard
rs11728110	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 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	chr4:57274200-57296400	Weak transcription	Dnd41	blood
7	chr4:57277000-57294200	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:57277000-57300000	Weak transcription	HSMM	muscle
10	chr4:57277800-57298000	Weak transcription	A549	lung
11	chr4:57278000-57294000	Weak transcription	HUVEC	blood vessel
12	chr4:57278000-57299200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:57278200-57300200	Weak transcription	Fetal Kidney	kidney
14	chr4:57278200-57300200	Weak transcription	NHDF-Ad	bronchial
15	chr4:57280600-57297800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:57280800-57299400	Weak transcription	Fetal Lung	lung
17	chr4:57281000-57295000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:57281000-57299200	Weak transcription	HMEC	breast
19	chr4:57284000-57294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:57284800-57300400	Weak transcription	Fetal Intestine Small	intestine
21	chr4:57286800-57297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:57287800-57299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:57288000-57297800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:57288000-57299200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:57289600-57299800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:57290200-57297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:57292000-57297800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:57292000-57299200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:57292200-57293400	Enhancers	GM12878-XiMat	blood
30	chr4:57292200-57295000	Weak transcription	HepG2	liver
31	chr4:57292200-57297600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:57292200-57298000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:57292200-57299200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:57292200-57299200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:57292200-57299200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:57292200-57299800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:57292400-57298000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:57292600-57293400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr4:57292600-57293800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:57292800-57293600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:57292800-57294000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:57293000-57293400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
43	chr4:57293000-57293800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:57293000-57294200	Strong transcription	K562	blood

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