Variant report

Variant	rs4888267
Chromosome Location	chr16:74687906-74687907
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	KAP1	chr16:74687893-74688371	K562	blood:	n/a	n/a
2	POLR2A	chr16:74687647-74689208	K562	blood:	n/a	n/a
3	RFX5	chr16:74687873-74688426	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74638965..74642242-chr16:74686896..74689511,3	MCF-7	breast:

Variant related genes	Relation type
RFWD3	TF binding region
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1019572	0.83[JPT][hapmap]
rs1019573	0.83[JPT][hapmap]
rs10500587	0.83[JPT][hapmap]
rs11639812	0.90[JPT][hapmap]
rs11644298	0.90[JPT][hapmap]
rs11648868	0.90[JPT][hapmap]
rs12325017	0.90[JPT][hapmap]
rs12446054	0.90[JPT][hapmap]
rs12448026	0.81[JPT][hapmap]
rs12598701	0.83[JPT][hapmap]
rs12716769	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12924948	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13339161	0.90[JPT][hapmap]
rs1469140	0.90[JPT][hapmap]
rs2098754	0.90[JPT][hapmap]
rs2288053	0.90[JPT][hapmap]
rs2303275	0.90[JPT][hapmap]
rs2303278	0.83[JPT][hapmap]
rs2303281	0.90[JPT][hapmap]
rs28681530	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785312	0.83[JPT][hapmap]
rs3826239	0.90[JPT][hapmap]
rs4072222	0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4438331	0.81[JPT][hapmap]
rs4887772	0.90[JPT][hapmap]
rs4887776	0.81[JPT][hapmap]
rs4887777	0.81[JPT][hapmap]
rs4887779	0.81[JPT][hapmap]
rs4888240	0.81[JPT][hapmap]
rs4888242	0.90[JPT][hapmap]
rs4888253	0.90[JPT][hapmap]
rs4888262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4888264	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4888265	0.84[CHB][hapmap];0.91[JPT][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4888274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56099065	0.85[AMR][1000 genomes]
rs57488599	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6564117	0.90[JPT][hapmap]
rs6564154	0.81[JPT][hapmap]
rs71376290	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7185026	0.90[JPT][hapmap]
rs7188581	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7188880	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7189123	0.90[JPT][hapmap]
rs7191665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7194143	0.81[JPT][hapmap]
rs7201320	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7204804	0.81[JPT][hapmap]
rs7205258	0.81[JPT][hapmap]
rs7342732	0.81[JPT][hapmap]
rs8050624	0.81[JPT][hapmap]
rs8052367	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8055784	0.81[JPT][hapmap]
rs8058133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8058692	0.81[JPT][hapmap]
rs8059780	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8059869	0.81[JPT][hapmap]
rs8061942	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8062783	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs918782	0.90[JPT][hapmap]
rs9922988	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9923145	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9923616	0.83[JPT][hapmap]
rs9927073	0.81[JPT][hapmap]
rs9929483	0.81[JPT][hapmap]
rs9929496	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9929931	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9930188	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9931225	0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9932831	0.81[JPT][hapmap]
rs9938833	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv572975	chr16:74677312-74702254	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4888267	RFWD3	cis	Esophagus Mucosa	GTEx
rs4888267	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs4888267	MLKL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74642200-74688800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:74647800-74691800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr16:74648800-74688400	Strong transcription	Dnd41	blood
4	chr16:74648800-74692200	Strong transcription	Fetal Thymus	thymus
5	chr16:74651000-74691200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr16:74652000-74692200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:74652200-74699000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr16:74653200-74690600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr16:74653200-74698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:74653400-74699000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr16:74654400-74689000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr16:74655200-74688600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:74656800-74699400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr16:74657000-74699200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr16:74657200-74699400	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr16:74657200-74699600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr16:74657400-74699200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr16:74657400-74699600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr16:74658200-74697200	Weak transcription	Fetal Brain Male	brain
20	chr16:74665800-74688200	Weak transcription	Stomach Mucosa	stomach
21	chr16:74666000-74692000	Weak transcription	Fetal Heart	heart
22	chr16:74667800-74688600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr16:74671600-74688400	Strong transcription	Hela-S3	cervix
24	chr16:74673600-74695400	Strong transcription	Fetal Muscle Leg	muscle
25	chr16:74676000-74688800	Strong transcription	GM12878-XiMat	blood
26	chr16:74676200-74692000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr16:74676400-74689200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr16:74676600-74691600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr16:74677000-74691600	Strong transcription	HepG2	liver
30	chr16:74678400-74691800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr16:74678600-74692800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr16:74678600-74699800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr16:74679400-74688400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr16:74679400-74692800	Weak transcription	Brain Substantia Nigra	brain
35	chr16:74679600-74692000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr16:74680200-74688800	Weak transcription	Brain Hippocampus Middle	brain
37	chr16:74680600-74692000	Weak transcription	Pancreas	Pancrea
38	chr16:74680800-74688400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr16:74681000-74689000	Strong transcription	Primary B cells from cord blood	blood
40	chr16:74682400-74690600	Weak transcription	Brain Angular Gyrus	brain
41	chr16:74682800-74688400	Weak transcription	Gastric	stomach
42	chr16:74682800-74691800	Weak transcription	Colonic Mucosa	Colon
43	chr16:74682800-74692000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr16:74682800-74692800	Weak transcription	Spleen	Spleen
45	chr16:74682800-74693400	Weak transcription	Right Ventricle	heart
46	chr16:74683000-74693000	Weak transcription	Esophagus	oesophagus
47	chr16:74683200-74688000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr16:74683200-74692200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr16:74683800-74690600	Weak transcription	Brain Germinal Matrix	brain
50	chr16:74683800-74692000	Weak transcription	Fetal Kidney	kidney

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