Variant report

Variant	rs4985460
Chromosome Location	chr16:69964374-69964375
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	RAD21	chr16:69963933-69964497	HepG2	liver:	n/a	chr16:69963984-69964003 chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
2	SMC3	chr16:69964088-69964453	HepG2	liver:	n/a	chr16:69964276-69964290
3	ZNF143	chr16:69964100-69964450	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr16:69964111-69964454	GM12878	blood:	n/a	n/a
5	RAD21	chr16:69964012-69964490	IMR90	lung:	n/a	chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
6	CTCF	chr16:69964144-69964418	MCF-7	breast:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
7	SMC3	chr16:69964067-69964450	GM12878	blood:	n/a	chr16:69964276-69964290
8	RCOR1	chr16:69964132-69964412	K562	blood:	n/a	n/a
9	CTCF	chr16:69964146-69964421	Gliobla	brain:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
10	CTCF	chr16:69964187-69964402	LNCaP	prostate:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
11	CTCF	chr16:69964128-69964432	Medullo	brain:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
12	CTCF	chr16:69964205-69964378	GM20000	blood:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
13	TBL1XR1	chr16:69964234-69964407	K562	blood:	n/a	n/a
14	CTCF	chr16:69964159-69964426	LNCaP	prostate:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
15	FOXM1	chr16:69963951-69964452	GM12878	blood:	n/a	n/a
16	CTCF	chr16:69963925-69964667	HCT-116	colon:	n/a	chr16:69964274-69964292 chr16:69963986-69963999 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
17	RAD21	chr16:69963973-69964540	ECC-1	luminal epithelium:	n/a	chr16:69963984-69964003 chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
18	CTCF	chr16:69964159-69964417	HepG2	liver:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
19	CTCF	chr16:69964144-69964431	Hela-S3	cervix:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
20	CTCF	chr16:69964171-69964421	GM10248	blood:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
21	RAD21	chr16:69964073-69964413	HepG2	liver:	n/a	chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
22	CTCF	chr16:69964169-69964431	GM10266	blood:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
23	CTCF	chr16:69964151-69964387	MCF-7	breast:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
24	CTCF	chr16:69964039-69964469	A549	lung:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
25	SMC3	chr16:69964056-69964451	K562	blood:	n/a	chr16:69964276-69964290
26	CTCF	chr16:69964158-69964397	ProgFib	skin:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
27	CTCF	chr16:69964122-69964417	NHEK	skin:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
28	RAD21	chr16:69964000-69964468	A549	lung:	n/a	chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
29	TBL1XR1	chr16:69964061-69964391	K562	blood:	n/a	n/a
30	RAD21	chr16:69964082-69964374	K562	blood:	n/a	chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
31	CTCF	chr16:69964113-69964419	GM19240	blood:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
32	RAD21	chr16:69963959-69964427	MCF-7	breast:	n/a	chr16:69963984-69964003 chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
33	RAD21	chr16:69964102-69964449	K562	blood:	n/a	chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
34	CTCF	chr16:69964136-69964386	MCF-7	breast:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
35	FOXM1	chr16:69964115-69964512	GM12878	blood:	n/a	n/a
36	CTCF	chr16:69964066-69964473	K562	blood:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
37	CTCF	chr16:69964147-69964420	GM13977	blood:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
38	CTCF	chr16:69964043-69964496	GM12878	blood:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
39	ZNF143	chr16:69964212-69964400	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr16:69964077-69964456	GM12878	blood:	n/a	chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
41	CTCF	chr16:69963958-69964409	GM12891	blood:	n/a	chr16:69964274-69964292 chr16:69963986-69963999 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
42	CTCF	chr16:69964088-69964413	ECC-1	luminal epithelium:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
43	CTCF	chr16:69964240-69964390	AG09319	gingival:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
44	CTCF	chr16:69964112-69964437	GM12892	blood:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
45	CTCF	chr16:69964166-69964423	HUVEC	blood vessel:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
46	RAD21	chr16:69964086-69964467	Hela-S3	cervix:	n/a	chr16:69964272-69964291 chr16:69964282-69964289 chr16:69964278-69964287
47	NFIC	chr16:69964052-69964387	HepG2	liver:	n/a	n/a
48	CTCF	chr16:69964177-69964407	Kidney_OC	kidney:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
49	CTCF	chr16:69964091-69964421	A549	lung:	n/a	chr16:69964274-69964292 chr16:69964279-69964287 chr16:69964276-69964289 chr16:69964269-69964290 chr16:69964275-69964291
50	MAZ	chr16:69963745-69964518	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:69743165..69743799-chr16:69964274..69965111,2	K562	blood:
2	chr16:69957939..69963004-chr16:69963560..69969238,6	K562	blood:
3	chr16:69964274..69964839-chr17:62576497..62577035,2	MCF-7	breast:

Variant related genes	Relation type
WWP2	TF binding region
MIR140	TF binding region
ENSG00000198373	Chromatin interaction
ENSG00000261602	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 39 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12149320	0.82[EUR][1000 genomes]
rs2270843	0.92[EUR][1000 genomes]
rs3192882	0.91[EUR][1000 genomes]
rs4985462	0.87[EUR][1000 genomes]

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	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak 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 miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv1792580	chr16:69950347-70005207	Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	esv1801278	chr16:69951043-70050770	Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv1829103	chr16:69951043-70050770	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
10	nsv1853	chr16:69962296-70268856	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:39)

SNP	Gene	Cis/trans	Tissue	Source
rs4985460	CLEC18C	cis	lung	GTEx
rs4985460	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs4985460	PDXDC2P	cis	Esophagus Muscularis	GTEx
rs4985460	RP11-419C5.2	cis	Artery Aorta	GTEx
rs4985460	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs4985460	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs4985460	CLEC18A	cis	lung	GTEx
rs4985460	PDXDC2P	cis	Muscle Skeletal	GTEx
rs4985460	RP11-419C5.2	cis	lung	GTEx
rs4985460	PDXDC2P	cis	Nerve Tibial	GTEx
rs4985460	CLEC18A	cis	Artery Aorta	GTEx
rs4985460	PDXDC2P	cis	Thyroid	GTEx
rs4985460	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4985460	CLEC18A	cis	Esophagus Muscularis	GTEx
rs4985460	PDXDC2P	cis	Artery Tibial	GTEx
rs4985460	CLEC18A	cis	Whole Blood	GTEx
rs4985460	RP11-419C5.2	cis	Whole Blood	GTEx
rs4985460	CLEC18A	cis	Thyroid	GTEx
rs4985460	CLEC18A	cis	Adipose Subcutaneous	GTEx
rs4985460	RP11-419C5.2	cis	Adipose Subcutaneous	GTEx
rs4985460	CLEC18A	cis	Artery Tibial	GTEx
rs4985460	PDXDC2P	cis	Esophagus Mucosa	GTEx
rs4985460	PDXDC2P	cis	Adipose Subcutaneous	GTEx
rs4985460	CLEC18C	cis	Whole Blood	GTEx
rs4985460	EXOSC6	cis	Muscle Skeletal	GTEx
rs4985460	EXOSC6	cis	Artery Tibial	GTEx
rs4985460	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs4985460	CLEC18C	cis	Thyroid	GTEx
rs4985460	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs4985460	RP11-419C5.2	cis	Artery Tibial	GTEx
rs4985460	CLEC18A	cis	Muscle Skeletal	GTEx
rs4985460	RP11-419C5.2	cis	Esophagus Mucosa	GTEx
rs4985460	RP11-419C5.2	cis	Esophagus Muscularis	GTEx
rs4985460	PDXDC2P	cis	Whole Blood	GTEx
rs4985460	PDXDC2P	cis	lung	GTEx
rs4985460	RP11-296I10.6	cis	lung	GTEx
rs4985460	RP11-419C5.2	cis	Thyroid	GTEx
rs4985460	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs4985460	RP11-419C5.2	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69911400-69970200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69924400-69965000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:69939000-69974000	Weak transcription	Fetal Brain Male	brain
4	chr16:69939600-69967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr16:69943200-69965600	Weak transcription	Brain Germinal Matrix	brain
6	chr16:69943600-69965000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr16:69943600-69967000	Weak transcription	Small Intestine	intestine
8	chr16:69945200-69964600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr16:69945600-69969400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr16:69947600-69977200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr16:69948200-69977400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr16:69948400-69977400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:69952200-69965000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr16:69952600-69976000	Weak transcription	Hela-S3	cervix
15	chr16:69952800-69965000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:69952800-69966800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr16:69953600-69974800	Weak transcription	A549	lung
18	chr16:69954400-69976000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:69956400-69975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr16:69957400-69964400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr16:69957400-69977400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr16:69957600-69975400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr16:69957800-69977200	Strong transcription	Fetal Intestine Small	intestine
24	chr16:69958000-69965000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr16:69958000-69965000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr16:69958200-69965000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr16:69958200-69965000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr16:69958200-69965200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr16:69958200-69965600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr16:69958200-69972800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr16:69958400-69969800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr16:69958800-69967200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:69959000-69965000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr16:69959000-69976400	Strong transcription	Thymus	Thymus
35	chr16:69959000-69977200	Strong transcription	Fetal Intestine Large	intestine
36	chr16:69959000-69977600	Strong transcription	Primary T cells from cord blood	blood
37	chr16:69959200-69975400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr16:69959400-69965800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr16:69959400-69976200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr16:69959600-69965200	Weak transcription	Right Ventricle	heart
41	chr16:69959600-69975200	Strong transcription	Fetal Thymus	thymus
42	chr16:69959600-69975600	Strong transcription	Fetal Stomach	stomach
43	chr16:69959800-69970400	Weak transcription	HUVEC	blood vessel
44	chr16:69960000-69966400	Weak transcription	Fetal Lung	lung
45	chr16:69960200-69964800	Weak transcription	Primary B cells from cord blood	blood
46	chr16:69960200-69967400	Weak transcription	HMEC	breast
47	chr16:69960200-69969800	Weak transcription	GM12878-XiMat	blood
48	chr16:69960200-69971600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr16:69960400-69965800	Weak transcription	Colon Smooth Muscle	Colon
50	chr16:69960600-69964600	Weak transcription	Liver	Liver

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