Variant report

Variant	rs4353138
Chromosome Location	chr1:46219803-46219804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr1:46218450-46219844	K562	blood:	n/a	n/a
2	SETDB1	chr1:46218207-46219807	U2OS	brain:	n/a	n/a
3	TEAD4	chr1:46217999-46219924	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46149977..46154848-chr1:46211592..46220262,26	K562	blood:
2	chr1:46219624..46221778-chr1:46224955..46227777,2	MCF-7	breast:
3	chr1:46213853..46218009-chr1:46218217..46220727,8	K562	blood:
4	chr1:46216677..46220436-chr1:46232703..46236378,4	K562	blood:
5	chr1:46213556..46220443-chr1:46266629..46271737,8	K562	blood:
6	chr1:46214695..46217951-chr1:46218434..46222667,10	K562	blood:
7	chr1:46150194..46156123-chr1:46211510..46222859,25	K562	blood:
8	chr1:46217664..46220133-chr1:46344829..46347460,2	K562	blood:
9	chr1:46216570..46222815-chr1:46224414..46229889,7	K562	blood:

No data

Variant related genes	Relation type
IPP	TF binding region
ENSG00000159596	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000197429	Chromatin interaction
ENSG00000086015	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11211188	0.80[EUR][1000 genomes]
rs11587650	0.81[EUR][1000 genomes]
rs12025621	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12027345	0.84[EUR][1000 genomes]
rs12045165	0.83[EUR][1000 genomes]
rs12404197	0.96[EUR][1000 genomes]
rs2230657	0.80[EUR][1000 genomes]
rs28378621	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28635845	0.94[EUR][1000 genomes]
rs28647556	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28844317	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2991985	0.85[EUR][1000 genomes]
rs3013594	0.90[EUR][1000 genomes]
rs3013595	0.94[EUR][1000 genomes]
rs3013596	0.91[EUR][1000 genomes]
rs3013597	0.94[EUR][1000 genomes]
rs3014238	0.85[EUR][1000 genomes]
rs3014243	0.97[EUR][1000 genomes]
rs3014247	0.93[EUR][1000 genomes]
rs4274104	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4391704	0.86[EUR][1000 genomes]
rs4468203	0.92[EUR][1000 genomes]
rs4660312	0.92[EUR][1000 genomes]
rs4660882	0.91[EUR][1000 genomes]
rs4660885	0.86[EUR][1000 genomes]
rs5021934	0.92[EUR][1000 genomes]
rs6429576	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6656279	0.93[EUR][1000 genomes]
rs6661163	0.83[EUR][1000 genomes]
rs6671802	0.94[EUR][1000 genomes]
rs6683500	0.83[EUR][1000 genomes]
rs6703960	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72688483	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv1010054	chr1:46144479-46320493	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 target site	75 gene(s)	inside rSNPs	diseases
8	nsv1006861	chr1:46144479-46417621	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
9	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv870511	chr1:46148138-46245423	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv871233	chr1:46153203-46311275	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
13	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
14	nsv1000498	chr1:46171836-46438252	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
15	nsv870791	chr1:46182916-46398415	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv871023	chr1:46184300-46301182	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv998925	chr1:46184925-46353041	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
18	nsv1003986	chr1:46184925-46417621	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
19	nsv1007501	chr1:46184925-46439533	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
20	nsv534944	chr1:46184925-46439533	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
21	nsv871763	chr1:46186576-46236098	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
22	nsv1006891	chr1:46189258-46408032	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
23	nsv1009355	chr1:46189258-46463012	Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
24	nsv870626	chr1:46196813-46314170	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
25	nsv871312	chr1:46196813-46353332	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
26	esv2830426	chr1:46202361-46347367	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
27	nsv546158	chr1:46216575-46495434	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
28	nsv870911	chr1:46216575-46498375	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4353138	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs4353138	MAST2	cis	Artery Aorta	GTEx
rs4353138	CCDC163P	cis	lung	GTEx
rs4353138	CCDC163P	cis	Heart Left Ventricle	GTEx
rs4353138	CCDC163P	cis	Artery Aorta	GTEx
rs4353138	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs4353138	CCDC163P	cis	Whole Blood	GTEx
rs4353138	GPBP1L1	cis	Whole Blood	GTEx
rs4353138	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs4353138	CCDC163P	cis	Artery Tibial	GTEx
rs4353138	CCDC163P	cis	Esophagus Muscularis	GTEx
rs4353138	MAST2	cis	Artery Tibial	GTEx
rs4353138	CCDC163P	cis	Stomach	GTEx
rs4353138	CCDC163P	cis	Esophagus Mucosa	GTEx
rs4353138	CCDC163P	cis	Thyroid	GTEx
rs4353138	CCDC163P	cis	Nerve Tibial	GTEx
rs4353138	CCDC163P	cis	Muscle Skeletal	GTEx
rs4353138	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46217200-46221000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:46219200-46220400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
3	chr1:46219200-46221000	Weak transcription	HepG2	liver
4	chr1:46219800-46221200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links