Variant report

Variant	rs4845557
Chromosome Location	chr1:153609039-153609040
allele	C/T
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	JUND	chr1:153608878-153609149	HepG2	liver:	n/a	chr1:153609000-153609009
2	SETDB1	chr1:153608702-153609297	U2OS	brain:	n/a	n/a
3	POLR2A	chr1:153608441-153609714	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153607039..153609365-chr1:153641782..153643312,2	K562	blood:
2	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:

Variant related genes	Relation type
CHTOP	TF binding region
ENSG00000272030	TF binding region
S100A13	TF binding region
ENSG00000271853	TF binding region
ENSG00000143621	Chromatin interaction
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1046381	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10797056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797090	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908746	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265633	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1128894	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11548103	0.82[EUR][1000 genomes]
rs11548104	0.82[EUR][1000 genomes]
rs11580122	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12139953	0.85[ASN][1000 genomes]
rs12564925	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730186	0.88[ASN][1000 genomes]
rs1411273	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1810836	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1888115	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274739	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274740	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379831	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28416529	0.85[EUR][1000 genomes]
rs28510471	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28518786	0.93[ASN][1000 genomes]
rs28580554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28613361	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28700217	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3790411	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3790412	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3806233	0.80[ASN][1000 genomes]
rs3806234	0.83[ASN][1000 genomes]
rs3818632	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828031	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862047	0.80[ASN][1000 genomes]
rs4351684	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845558	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845560	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845563	0.85[ASN][1000 genomes]
rs6427640	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66721814	0.85[ASN][1000 genomes]
rs6694006	0.85[AMR][1000 genomes]
rs7345	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7934	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913860	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs913861	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9330299	0.82[EUR][1000 genomes]
rs9330300	0.82[EUR][1000 genomes]
rs9330301	0.83[EUR][1000 genomes]
rs9661993	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9729773	0.82[EUR][1000 genomes]
rs985242	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs999418	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4845557	S100A13	cis	Adipose Subcutaneous	GTEx
rs4845557	CHTOP	cis	Muscle Skeletal	GTEx
rs4845557	RP1-178F15.4	cis	Artery Aorta	GTEx
rs4845557	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs4845557	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs4845557	RP1-178F15.4	cis	lung	GTEx
rs4845557	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs4845557	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs4845557	RP1-178F15.4	cis	Heart Left Ventricle	GTEx
rs4845557	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153607200-153610200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:153607600-153609600	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr1:153607800-153609200	Enhancers	Fetal Brain Male	brain
4	chr1:153607800-153609600	Genic enhancers	Primary B cells from peripheral blood	blood
5	chr1:153608000-153609200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:153608000-153609200	Enhancers	Fetal Heart	heart
7	chr1:153608000-153609800	Genic enhancers	NHEK	skin
8	chr1:153608000-153611200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:153608000-153611600	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr1:153608200-153609200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:153608200-153609200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:153608200-153609400	Genic enhancers	Thymus	Thymus
13	chr1:153608200-153609600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:153608200-153609600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr1:153608200-153609600	Genic enhancers	Fetal Stomach	stomach
16	chr1:153608200-153609600	Genic enhancers	Rectal Smooth Muscle	rectum
17	chr1:153608200-153609600	Enhancers	Right Atrium	heart
18	chr1:153608200-153609600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:153608200-153609600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
20	chr1:153608200-153609800	Genic enhancers	HepG2	liver
21	chr1:153608200-153610000	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr1:153608200-153610000	Genic enhancers	Lung	lung
23	chr1:153608200-153610200	Genic enhancers	Fetal Muscle Leg	muscle
24	chr1:153608200-153610800	Genic enhancers	Adipose Nuclei	Adipose
25	chr1:153608200-153611000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:153608200-153611000	Genic enhancers	Fetal Intestine Small	intestine
27	chr1:153608200-153611000	Enhancers	Stomach Mucosa	stomach
28	chr1:153608200-153611800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:153608200-153613200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:153608200-153618600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:153608200-153618800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:153608200-153619600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:153608400-153609200	Genic enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:153608400-153609200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:153608400-153609200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:153608400-153609200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:153608400-153609200	Genic enhancers	Spleen	Spleen
38	chr1:153608400-153609200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
39	chr1:153608400-153609400	Genic enhancers	Colonic Mucosa	Colon
40	chr1:153608400-153609600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:153608400-153609600	Genic enhancers	Colon Smooth Muscle	Colon
42	chr1:153608400-153609600	Genic enhancers	Placenta	Placenta
43	chr1:153608400-153609600	Transcr. at gene 5' and 3'	Hela-S3	cervix
44	chr1:153608400-153609800	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr1:153608400-153610600	Genic enhancers	Brain Anterior Caudate	brain
46	chr1:153608400-153616400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:153608400-153618600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:153608400-153618800	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr1:153608400-153618800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:153608400-153619200	Strong transcription	HUES48 Cell Line	embryonic stem cell

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