Variant report

Variant	rs4462623
Chromosome Location	chr16:74692426-74692427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74679071..74680633-chr16:74691530..74693953,2	K562	blood:
2	chr16:74691160..74693410-chr16:74694917..74697832,4	MCF-7	breast:
3	chr16:74690546..74692876-chr16:74698874..74700526,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168411	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10400930	0.88[ASN][1000 genomes]
rs1138860	0.81[ASN][1000 genomes]
rs12921903	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12935075	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13339156	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28377859	0.89[ASN][1000 genomes]
rs28502731	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4072222	0.93[ASN][1000 genomes]
rs4072450	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4243108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4271617	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4286131	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4287593	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4302071	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4344772	0.83[ASN][1000 genomes]
rs4544266	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4548905	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4564599	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4588013	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4887776	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4887777	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4887779	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4888257	0.83[ASN][1000 genomes]
rs4888258	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4888259	0.87[ASN][1000 genomes]
rs4888266	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4888270	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57488599	0.93[ASN][1000 genomes]
rs58136167	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6564145	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6564146	0.86[ASN][1000 genomes]
rs6564147	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6564148	0.87[ASN][1000 genomes]
rs6564149	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6564152	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6564153	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6564154	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6564155	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6564157	0.88[ASN][1000 genomes]
rs7184754	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7185722	0.89[ASN][1000 genomes]
rs7190631	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7193423	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7193508	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7193583	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7193959	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7194687	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7195135	0.84[ASN][1000 genomes]
rs7195499	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7196627	0.82[EUR][1000 genomes]
rs7204382	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7204804	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7205258	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7342732	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8047243	0.85[ASN][1000 genomes]
rs8047523	0.83[EUR][1000 genomes]
rs8048596	0.83[ASN][1000 genomes]
rs8049056	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8050615	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8050624	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8052923	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8053084	0.86[ASN][1000 genomes]
rs8055784	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8055803	0.85[ASN][1000 genomes]
rs8056718	0.87[ASN][1000 genomes]
rs8057279	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8058034	0.88[ASN][1000 genomes]
rs8058437	0.85[ASN][1000 genomes]
rs8058922	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8062404	0.87[ASN][1000 genomes]
rs8062959	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9921672	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9925807	0.86[ASN][1000 genomes]
rs9927073	0.85[ASN][1000 genomes]
rs9928181	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9929483	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9931225	0.91[ASN][1000 genomes]
rs9938833	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[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	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
11	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4462623	RFWD3	Cis_1M	lymphoblastoid	RTeQTL
rs4462623	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs4462623	RFWD3	cis	Skin Sun Exposed Lower leg	GTEx
rs4462623	RFWD3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74652200-74699000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:74653200-74698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:74653400-74699000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr16:74656800-74699400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:74657000-74699200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:74657200-74699400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr16:74657200-74699600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr16:74657400-74699200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:74657400-74699600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr16:74658200-74697200	Weak transcription	Fetal Brain Male	brain
11	chr16:74673600-74695400	Strong transcription	Fetal Muscle Leg	muscle
12	chr16:74678600-74692800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr16:74678600-74699800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr16:74679400-74692800	Weak transcription	Brain Substantia Nigra	brain
15	chr16:74682800-74692800	Weak transcription	Spleen	Spleen
16	chr16:74682800-74693400	Weak transcription	Right Ventricle	heart
17	chr16:74683000-74693000	Weak transcription	Esophagus	oesophagus
18	chr16:74684400-74692800	Weak transcription	NHLF	lung
19	chr16:74684800-74694800	Weak transcription	Psoas Muscle	Psoas
20	chr16:74685000-74700000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr16:74685800-74699400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr16:74686000-74692800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:74686000-74693000	Weak transcription	Colon Smooth Muscle	Colon
24	chr16:74686200-74694400	Weak transcription	Small Intestine	intestine
25	chr16:74686400-74692800	Weak transcription	Brain Anterior Caudate	brain
26	chr16:74686400-74693000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr16:74686400-74693200	Weak transcription	NHDF-Ad	bronchial
28	chr16:74687200-74692800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr16:74687200-74699800	Weak transcription	Right Atrium	heart
30	chr16:74687800-74694000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr16:74688000-74699200	Strong transcription	Placenta	Placenta
32	chr16:74688000-74699400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr16:74688200-74695600	Strong transcription	Fetal Stomach	stomach
34	chr16:74688200-74695800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr16:74688200-74695800	Strong transcription	Fetal Intestine Large	intestine
36	chr16:74688400-74695400	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr16:74688800-74693000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr16:74689000-74693000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr16:74689000-74698800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr16:74689200-74692800	Weak transcription	Gastric	stomach
41	chr16:74689200-74699600	Strong transcription	Fetal Intestine Small	intestine
42	chr16:74689200-74699800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr16:74689400-74699200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:74689600-74699200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:74689800-74699600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr16:74690000-74699400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr16:74690200-74694400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr16:74690200-74699000	Strong transcription	Fetal Brain Female	brain
49	chr16:74690400-74693000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr16:74690400-74693200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood

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