Variant report

Variant	rs4588013
Chromosome Location	chr16:74703388-74703389
allele	C/T
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	chr16:74703123-74703655	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr16:74702029-74704476	MCF10A-Er-Src	breast:	n/a	n/a
3	IRF1	chr16:74703337-74703537	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:74701971..74704127-chr16:74845160..74847638,2	MCF-7	breast:
2	chr16:74700450..74705009-chr16:74710570..74714672,7	MCF-7	breast:
3	chr16:74701472..74703835-chr16:74735613..74737819,2	K562	blood:

Variant related genes	Relation type
RFWD3	TF binding region
ENSG00000168404	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12921903	0.84[EUR][1000 genomes]
rs12935075	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13339156	0.83[EUR][1000 genomes]
rs4072222	0.88[ASN][1000 genomes]
rs4072450	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4243108	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4271617	0.83[ASN][1000 genomes]
rs4286131	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4287593	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4462623	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4476202	0.82[ASN][1000 genomes]
rs4548905	0.84[EUR][1000 genomes]
rs4564599	0.81[AFR][1000 genomes]
rs4887776	0.83[EUR][1000 genomes]
rs4887777	0.84[EUR][1000 genomes]
rs4887779	0.85[EUR][1000 genomes]
rs4888258	0.83[EUR][1000 genomes]
rs4888266	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4888270	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57488599	0.88[ASN][1000 genomes]
rs58136167	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6564147	0.81[EUR][1000 genomes]
rs6564149	0.82[EUR][1000 genomes]
rs6564152	0.81[AFR][1000 genomes]
rs6564153	0.81[AFR][1000 genomes]
rs6564154	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6564155	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6564157	0.91[ASN][1000 genomes]
rs7184754	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7190631	0.83[AFR][1000 genomes]
rs7193423	0.83[EUR][1000 genomes]
rs7193508	0.83[EUR][1000 genomes]
rs7193583	0.85[EUR][1000 genomes]
rs7193959	0.86[EUR][1000 genomes]
rs7194687	0.85[EUR][1000 genomes]
rs7195499	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7196627	0.81[EUR][1000 genomes]
rs7204382	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7205258	0.81[EUR][1000 genomes]
rs7342732	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8047523	0.81[EUR][1000 genomes]
rs8050624	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8052923	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8055784	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8057279	0.82[EUR][1000 genomes]
rs8058922	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs8062959	0.83[EUR][1000 genomes]
rs9921672	0.84[EUR][1000 genomes]
rs9928181	0.81[EUR][1000 genomes]
rs9929483	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9931225	0.82[ASN][1000 genomes]
rs9938833	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	esv275138	chr16:74647795-74722907	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv2760414	chr16:74647795-74741615	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
8	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
9	nsv906906	chr16:74664743-74805668	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
10	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
11	nsv906907	chr16:74702254-74785902	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking 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	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4588013	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs4588013	RFWD3	cis	Thyroid	GTEx
rs4588013	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs4588013	RFWD3	cis	Esophagus Mucosa	GTEx
rs4588013	RFWD3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74700800-74705800	Weak transcription	Spleen	Spleen
2	chr16:74701400-74706000	Weak transcription	Small Intestine	intestine
3	chr16:74701600-74705400	Weak transcription	Lung	lung
4	chr16:74701600-74705400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr16:74701600-74705800	Weak transcription	Aorta	Aorta
6	chr16:74701600-74705800	Weak transcription	Esophagus	oesophagus
7	chr16:74701600-74705800	Weak transcription	Gastric	stomach
8	chr16:74701600-74712000	Weak transcription	Pancreas	Pancrea
9	chr16:74701600-74730000	Weak transcription	Stomach Mucosa	stomach
10	chr16:74701800-74705200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:74701800-74705200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:74701800-74705400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr16:74701800-74705400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr16:74701800-74705400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr16:74701800-74705400	Weak transcription	HMEC	breast
16	chr16:74701800-74705600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr16:74701800-74705600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr16:74701800-74705600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr16:74701800-74705600	Weak transcription	Adipose Nuclei	Adipose
20	chr16:74701800-74705600	Weak transcription	Left Ventricle	heart
21	chr16:74701800-74705800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr16:74701800-74705800	Weak transcription	Colonic Mucosa	Colon
23	chr16:74701800-74705800	Weak transcription	HUVEC	blood vessel
24	chr16:74701800-74706600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr16:74701800-74707200	Weak transcription	Fetal Intestine Small	intestine
26	chr16:74701800-74708800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr16:74701800-74709000	Weak transcription	Fetal Stomach	stomach
28	chr16:74701800-74709400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr16:74701800-74710000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr16:74701800-74711400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:74701800-74712800	Weak transcription	Placenta	Placenta
32	chr16:74701800-74715400	Weak transcription	Brain Angular Gyrus	brain
33	chr16:74701800-74724600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr16:74701800-74725400	Weak transcription	Ovary	ovary
35	chr16:74701800-74725400	Weak transcription	NHLF	lung
36	chr16:74701800-74729600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr16:74701800-74729800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr16:74701800-74730000	Weak transcription	Brain Substantia Nigra	brain
39	chr16:74701800-74734000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr16:74702000-74705000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr16:74702000-74705200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr16:74702000-74705400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr16:74702000-74705400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr16:74702000-74705400	Weak transcription	Primary T cells from cord blood	blood
45	chr16:74702000-74705400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr16:74702000-74705400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr16:74702000-74705400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr16:74702000-74705400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:74702000-74705400	Weak transcription	Liver	Liver
50	chr16:74702000-74705400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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