Variant report

Variant	rs41265162
Chromosome Location	chr1:153520138-153520139
allele	C/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:9)
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	POLR2A	chr1:153518799-153520253	SK-N-MC	brain:	n/a	n/a
2	MAX	chr1:153519677-153520169	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr1:153519483-153522520	A549	lung:	n/a	chr1:153520680-153520690
4	POLR2A	chr1:153517452-153526571	MCF10A-Er-Src	breast:	n/a	n/a
5	E2F6	chr1:153519664-153520179	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:153518586..153521432-chr1:153521639..153523247,2	K562	blood:
2	chr1:153519598..153522352-chr1:153580214..153582486,2	K562	blood:
3	chr1:153518882..153521795-chr1:153587475..153590405,3	MCF-7	breast:
4	chr1:153518586..153521432-chr1:153521623..153523247,3	K562	blood:
5	chr1:153514095..153517799-chr1:153518495..153521571,4	K562	blood:
6	chr1:153519212..153523090-chr1:153584863..153588698,4	MCF-7	breast:
7	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
8	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:
9	chr1:153327754..153330695-chr1:153517590..153520533,2	K562	blood:

No data

Variant related genes	Relation type
S100A4	TF binding region
ENSG00000163220	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000189334	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	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28548347	0.84[AFR][1000 genomes];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	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36022742	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762268	0.94[EUR][1000 genomes]
rs41265160	0.96[AFR][1000 genomes]
rs41265164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4595398	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55955983	0.94[EUR][1000 genomes]
rs56043239	1.00[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	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56350425	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56838169	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57024596	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58056804	0.97[EUR][1000 genomes]
rs58072118	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59376279	0.86[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61265945	0.82[AFR][1000 genomes];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	0.98[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:103 , 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	chr1:153516200-153520600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:153516800-153520400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:153516800-153521800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:153516800-153522000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:153516800-153522400	Enhancers	Fetal Intestine Small	intestine
10	chr1:153517200-153522400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:153517400-153524000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:153517600-153522800	Enhancers	Spleen	Spleen
13	chr1:153518000-153522600	Enhancers	Fetal Stomach	stomach
14	chr1:153518200-153521000	Weak transcription	HUVEC	blood vessel
15	chr1:153518200-153521800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:153518200-153521800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:153518200-153523000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:153518200-153524000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:153518200-153524000	Enhancers	K562	blood
20	chr1:153518400-153520200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:153518400-153520400	Flanking Active TSS	Hela-S3	cervix
22	chr1:153518400-153521000	Weak transcription	NH-A	brain
23	chr1:153518400-153522200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:153518400-153522800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:153518400-153523800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:153518600-153520600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:153518600-153521000	Weak transcription	Osteobl	bone
28	chr1:153518600-153521200	Enhancers	HSMM	muscle
29	chr1:153518600-153521400	Weak transcription	Psoas Muscle	Psoas
30	chr1:153518600-153521400	Weak transcription	Small Intestine	intestine
31	chr1:153518600-153521600	Weak transcription	GM12878-XiMat	blood
32	chr1:153518600-153521800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:153518600-153522000	Weak transcription	Gastric	stomach
34	chr1:153518600-153522400	Weak transcription	Fetal Lung	lung
35	chr1:153518600-153522400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:153518600-153522800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:153518600-153523600	Enhancers	Fetal Thymus	thymus
38	chr1:153518600-153524000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr1:153518600-153524000	Enhancers	Placenta	Placenta
40	chr1:153518600-153524200	Enhancers	Lung	lung
41	chr1:153518800-153520200	Enhancers	Primary T cells from cord blood	blood
42	chr1:153518800-153520200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:153518800-153520200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:153518800-153520200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr1:153518800-153521600	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr1:153518800-153523200	Enhancers	Right Atrium	heart
47	chr1:153518800-153524200	Enhancers	Esophagus	oesophagus
48	chr1:153519000-153520200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr1:153519000-153520400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:153519000-153520400	Enhancers	Primary T helper cells fromperipheralblood	blood

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