Variant report

Variant	rs56838169
Chromosome Location	chr1:153518783-153518784
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr1:153517420-153518905	Hela-S3	cervix:	n/a	n/a
2	MAZ	chr1:153517249-153519081	IMR90	lung:	n/a	n/a
3	TCF12	chr1:153516679-153519108	A549	lung:	n/a	n/a
4	POLR2A	chr1:153517452-153526571	MCF10A-Er-Src	breast:	n/a	n/a
5	GTF3C2	chr1:153518601-153518948	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153518586..153521432-chr1:153521639..153523247,2	K562	blood:
2	chr1:153518586..153521432-chr1:153521623..153523247,3	K562	blood:
3	chr1:153517686..153519228-chr1:153538736..153541189,3	K562	blood:
4	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
5	chr1:153514095..153517799-chr1:153518495..153521571,4	K562	blood:
6	chr1:153517525..153519027-chr1:153598182..153599900,2	K562	blood:
7	chr1:153508634..153510673-chr1:153516202..153519160,2	K562	blood:
8	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
9	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:
10	chr1:153327754..153330695-chr1:153517590..153520533,2	K562	blood:

No data

Variant related genes	Relation type
S100A5	TF binding region
S100A4	TF binding region
ENSG00000188643	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000188015	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1047325	0.91[EUR][1000 genomes]
rs1050923	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11488669	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835437	0.91[EUR][1000 genomes]
rs16835455	0.91[EUR][1000 genomes]
rs1810765	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28452456	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28548347	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594230	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28689606	0.97[EUR][1000 genomes]
rs28718953	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36022742	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762268	0.94[EUR][1000 genomes]
rs41265160	0.91[AFR][1000 genomes]
rs41265162	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41265164	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4595398	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55955983	0.94[EUR][1000 genomes]
rs56043239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56057245	0.84[EUR][1000 genomes]
rs56089062	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56350425	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57024596	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58056804	0.97[EUR][1000 genomes]
rs58072118	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59376279	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60218214	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60287468	0.97[EUR][1000 genomes]
rs60969679	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61265945	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61558997	0.91[EUR][1000 genomes]
rs6427301	0.94[EUR][1000 genomes]
rs6671398	0.88[EUR][1000 genomes]
rs6700310	0.91[EUR][1000 genomes]
rs73026350	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115473	0.97[EUR][1000 genomes]
rs74115476	0.91[EUR][1000 genomes]
rs743687	0.82[EUR][1000 genomes]
rs7535476	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8401	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS 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 miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153509400-153527600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:153512400-153522400	Enhancers	Stomach Mucosa	stomach
3	chr1:153515400-153522800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:153515400-153523000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:153515600-153518800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr1:153515600-153520000	Enhancers	HMEC	breast
7	chr1:153516200-153520600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:153516400-153518800	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr1:153516400-153519000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:153516600-153519000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr1:153516800-153518800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr1:153516800-153518800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr1:153516800-153518800	Flanking Active TSS	Esophagus	oesophagus
14	chr1:153516800-153518800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr1:153516800-153519000	Enhancers	Fetal Intestine Large	intestine
16	chr1:153516800-153519200	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr1:153516800-153519600	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr1:153516800-153520400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:153516800-153521800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:153516800-153522000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:153516800-153522400	Enhancers	Fetal Intestine Small	intestine
22	chr1:153517000-153518800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:153517000-153519000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:153517000-153519800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:153517000-153519800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:153517000-153519800	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr1:153517200-153518800	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr1:153517200-153518800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:153517200-153518800	Active TSS	Placenta Amnion	Placenta Amnion
30	chr1:153517200-153519000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:153517200-153519000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:153517200-153519200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr1:153517200-153519400	Active TSS	Aorta	Aorta
34	chr1:153517200-153519400	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr1:153517200-153519800	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr1:153517200-153522400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:153517400-153518800	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr1:153517400-153518800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:153517400-153518800	Flanking Active TSS	NHLF	lung
40	chr1:153517400-153519000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr1:153517400-153519200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:153517400-153519200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr1:153517400-153524000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:153517600-153519000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:153517600-153519600	Enhancers	NHEK	skin
46	chr1:153517600-153522800	Enhancers	Spleen	Spleen
47	chr1:153518000-153518800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:153518000-153519000	Active TSS	NHDF-Ad	bronchial
49	chr1:153518000-153519200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:153518000-153519200	Enhancers	Dnd41	blood

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