Variant report

Variant	rs4888262
Chromosome Location	chr16:74670458-74670459
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	chr16:74670174-74670483	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr16:74669386-74670482	K562	blood:	n/a	n/a
3	POLR2A	chr16:74670225-74670463	HL-60	blood:	n/a	n/a
4	POLR2A	chr16:74670207-74670466	K562	blood:	n/a	n/a

Variant related genes	Relation type
RFWD3	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1019572	0.92[JPT][hapmap]
rs1019573	0.92[JPT][hapmap]
rs10500587	0.92[JPT][hapmap]
rs11149722	0.92[JPT][hapmap]
rs11639812	0.92[JPT][hapmap]
rs11644298	0.92[JPT][hapmap]
rs11648868	0.92[JPT][hapmap]
rs12325017	0.92[JPT][hapmap]
rs12445991	0.85[JPT][hapmap]
rs12446054	0.92[JPT][hapmap]
rs12448026	0.85[JPT][hapmap];0.85[MKK][hapmap]
rs12598701	0.92[JPT][hapmap]
rs12716769	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12924948	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13339161	0.92[JPT][hapmap]
rs13359	0.92[JPT][hapmap]
rs1469140	0.92[JPT][hapmap]
rs2098754	0.92[JPT][hapmap];0.83[MKK][hapmap]
rs2288053	0.92[JPT][hapmap]
rs2303275	0.92[JPT][hapmap]
rs2303278	0.92[JPT][hapmap]
rs2303281	0.92[JPT][hapmap]
rs28681530	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3785312	0.92[JPT][hapmap]
rs3826239	0.92[JPT][hapmap]
rs3851729	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4072222	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4243108	0.90[MKK][hapmap]
rs4438331	0.85[JPT][hapmap]
rs4887772	0.92[JPT][hapmap]
rs4887776	0.85[JPT][hapmap]
rs4887777	0.85[JPT][hapmap]
rs4887779	0.85[JPT][hapmap]
rs4888238	0.92[JPT][hapmap]
rs4888240	0.85[JPT][hapmap]
rs4888242	0.92[JPT][hapmap]
rs4888253	0.92[JPT][hapmap]
rs4888256	0.85[MKK][hapmap]
rs4888264	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888265	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4888266	0.85[JPT][hapmap]
rs4888267	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]
rs4888274	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56099065	0.81[AMR][1000 genomes]
rs57488599	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6564117	0.92[JPT][hapmap]
rs6564154	0.85[JPT][hapmap];0.86[MKK][hapmap]
rs71376290	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7185026	0.92[JPT][hapmap];0.85[MKK][hapmap]
rs7188581	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7188880	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7189123	0.92[JPT][hapmap]
rs7191665	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7193959	0.85[JPT][hapmap]
rs7194143	0.85[JPT][hapmap]
rs7201320	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7203452	0.85[MKK][hapmap]
rs7204382	0.86[MKK][hapmap]
rs7204804	0.85[JPT][hapmap];0.85[MKK][hapmap]
rs7205258	0.85[JPT][hapmap]
rs7342732	0.85[JPT][hapmap];0.90[MKK][hapmap]
rs7978	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8050624	0.85[JPT][hapmap];0.90[MKK][hapmap]
rs8052367	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8052923	0.85[JPT][hapmap]
rs8055784	0.85[JPT][hapmap];0.87[MKK][hapmap]
rs8058133	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8058692	0.85[JPT][hapmap];0.85[MKK][hapmap]
rs8058922	0.87[MKK][hapmap]
rs8059780	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8059869	0.85[JPT][hapmap]
rs8061942	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8062783	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs918782	0.92[JPT][hapmap];0.85[MKK][hapmap]
rs9922988	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9923145	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9923616	0.92[JPT][hapmap]
rs9927073	0.85[JPT][hapmap];0.83[MKK][hapmap]
rs9929483	0.85[JPT][hapmap]
rs9929496	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9929931	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9930188	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9931225	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9932831	0.85[JPT][hapmap]
rs9938833	0.85[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	nsv906905	chr16:74527618-74679244	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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

Variant related diseases (count:1)

Disease	PMID	Source
Testicular germ cell tumor	23666239	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4888262	MLKL	cis	multi-tissue	Pritchard
rs4888262	RFWD3	cis	parietal	SCAN
rs4888262	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs4888262	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs4888262	RFWD3	cis	Esophagus Mucosa	GTEx
rs4888262	CYB5B	cis	parietal	SCAN
rs4888262	RFWD3	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 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	chr16:74650800-74687400	Strong transcription	Thymus	Thymus
6	chr16:74651000-74691200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr16:74652000-74674600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr16:74652000-74686000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr16:74652000-74692200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:74652200-74685600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:74652200-74687400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr16:74652200-74699000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:74653000-74686800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr16:74653000-74687800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:74653200-74683000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:74653200-74685600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr16:74653200-74687200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr16:74653200-74687800	Strong transcription	Fetal Stomach	stomach
19	chr16:74653200-74690600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr16:74653200-74698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:74653400-74670600	Strong transcription	A549	lung
22	chr16:74653400-74672000	Strong transcription	Fetal Muscle Leg	muscle
23	chr16:74653400-74699000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr16:74653600-74677800	Weak transcription	Psoas Muscle	Psoas
25	chr16:74654000-74685800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr16:74654400-74670600	Strong transcription	HMEC	breast
27	chr16:74654400-74689000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr16:74654600-74673400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr16:74654600-74686000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr16:74654600-74687800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr16:74654800-74672200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr16:74655000-74671600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr16:74655200-74673600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr16:74655200-74688600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr16:74655400-74670600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr16:74655400-74673600	Strong transcription	Lung	lung
37	chr16:74655400-74686000	Strong transcription	Placenta	Placenta
38	chr16:74655600-74672000	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr16:74655800-74670800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr16:74655800-74672000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr16:74655800-74672000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr16:74656200-74673400	Strong transcription	HUVEC	blood vessel
43	chr16:74656800-74699400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr16:74657000-74699200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr16:74657200-74699400	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr16:74657200-74699600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr16:74657400-74684600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr16:74657400-74699200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr16:74657400-74699600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr16:74657600-74685800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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