Variant report

Variant	rs4845558
Chromosome Location	chr1:153611563-153611564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
2	chr1:153610724..153613388-chr1:153700674..153702606,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196754	Chromatin interaction
ENSG00000143624	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1046381	0.87[EUR][1000 genomes]
rs10797056	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10797090	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10908746	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11265633	0.81[EUR][1000 genomes]
rs1128894	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11580122	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12564925	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1810836	0.88[EUR][1000 genomes]
rs1888115	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274739	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274740	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28379831	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28380060	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28510471	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28518786	0.81[ASN][1000 genomes]
rs28580554	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28613361	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28700217	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3790412	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795396	0.84[EUR][1000 genomes]
rs3818632	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3828031	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4351684	0.84[EUR][1000 genomes]
rs4845557	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6427640	0.84[EUR][1000 genomes]
rs7345	0.84[EUR][1000 genomes]
rs7934	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs913860	0.88[EUR][1000 genomes]
rs913861	0.88[EUR][1000 genomes];0.83[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4845558	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs4845558	CHTOP	cis	Muscle Skeletal	GTEx
rs4845558	RP1-178F15.4	cis	Heart Left Ventricle	GTEx
rs4845558	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs4845558	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs4845558	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs4845558	RP1-178F15.4	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153608000-153611600	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr1:153608200-153611800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:153608200-153613200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:153608200-153618600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:153608200-153618800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:153608200-153619600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:153608400-153616400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:153608400-153618600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:153608400-153618800	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr1:153608400-153618800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:153608400-153619200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:153608400-153619200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:153608400-153619800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:153608600-153615600	Strong transcription	Fetal Intestine Large	intestine
15	chr1:153608600-153618600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:153608600-153618800	Strong transcription	HUVEC	blood vessel
17	chr1:153608600-153619400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:153608600-153619400	Strong transcription	Osteobl	bone
19	chr1:153608600-153619600	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:153608600-153619600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:153608600-153619600	Strong transcription	HMEC	breast
22	chr1:153608600-153620200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:153608600-153620200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:153608800-153611600	Genic enhancers	Left Ventricle	heart
25	chr1:153608800-153612200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:153608800-153618400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:153608800-153618800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:153608800-153619400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:153608800-153619800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr1:153608800-153620200	Strong transcription	Fetal Thymus	thymus
31	chr1:153609000-153613000	Strong transcription	Fetal Kidney	kidney
32	chr1:153609000-153616200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:153609000-153616600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:153609000-153617000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:153609000-153618600	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr1:153609200-153612200	Genic enhancers	Fetal Heart	heart
37	chr1:153609200-153613000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:153609200-153614600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:153609200-153617600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:153609200-153618800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:153609200-153619400	Strong transcription	Spleen	Spleen
42	chr1:153609200-153620000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:153609200-153620000	Strong transcription	Fetal Brain Female	brain
44	chr1:153609200-153620200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:153609400-153612200	Strong transcription	Colonic Mucosa	Colon
46	chr1:153609400-153618800	Strong transcription	Fetal Lung	lung
47	chr1:153609400-153618800	Strong transcription	NH-A	brain
48	chr1:153609400-153619000	Strong transcription	Thymus	Thymus
49	chr1:153609600-153611600	Strong transcription	Right Ventricle	heart
50	chr1:153609600-153611600	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links