Variant report

Variant	rs1810836
Chromosome Location	chr1:153620223-153620224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153505419..153507126-chr1:153619348..153622269,2	K562	blood:
2	chr1:153542770..153546215-chr1:153620036..153623245,5	MCF-7	breast:
3	chr1:153616510..153622201-chr1:153629664..153635649,10	MCF-7	breast:
4	chr1:153619364..153621640-chr1:153746906..153749377,2	MCF-7	breast:
5	chr1:153619135..153622133-chr1:153720546..153722065,2	K562	blood:

Variant related genes	Relation type
ENSG00000143553	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1046381	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10797056	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10797090	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908746	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11265633	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1128894	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11548103	0.82[EUR][1000 genomes]
rs11548104	0.82[EUR][1000 genomes]
rs11580122	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12139953	0.80[ASN][1000 genomes]
rs12564925	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12730186	0.81[ASN][1000 genomes]
rs1411273	0.80[EUR][1000 genomes]
rs1888115	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2274739	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2274740	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28379831	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28380060	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28416529	0.84[EUR][1000 genomes]
rs28510471	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28580554	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28613361	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28700217	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3790411	0.82[EUR][1000 genomes]
rs3790412	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3795396	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3818632	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3828031	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4351684	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4845557	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845558	0.88[EUR][1000 genomes]
rs4845560	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845563	0.80[ASN][1000 genomes]
rs6427640	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66721814	0.80[ASN][1000 genomes]
rs6694006	0.81[AMR][1000 genomes]
rs7345	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7934	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs913860	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs913861	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9330299	0.82[EUR][1000 genomes]
rs9330300	0.81[EUR][1000 genomes]
rs9330301	0.83[EUR][1000 genomes]
rs9661993	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9729773	0.82[EUR][1000 genomes]
rs985242	0.80[EUR][1000 genomes]
rs999418	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1810836	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs1810836	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs1810836	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs1810836	RP1-178F15.4	cis	Heart Left Ventricle	GTEx
rs1810836	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs1810836	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs1810836	RP1-178F15.4	cis	Artery Aorta	GTEx
rs1810836	CHTOP	cis	Muscle Skeletal	GTEx
rs1810836	S100A13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153609600-153620800	Strong transcription	Fetal Stomach	stomach
2	chr1:153611000-153622400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:153615000-153620400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:153617400-153620400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:153617400-153620800	Strong transcription	Fetal Intestine Small	intestine
6	chr1:153617600-153620600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:153618400-153620600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:153618400-153621600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:153618400-153621800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:153618400-153625400	Weak transcription	Small Intestine	intestine
11	chr1:153618400-153630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:153618400-153631200	Weak transcription	Aorta	Aorta
13	chr1:153618600-153620600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:153618600-153620800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:153618600-153621200	Enhancers	Adipose Nuclei	Adipose
16	chr1:153618600-153621600	Weak transcription	Brain Angular Gyrus	brain
17	chr1:153618600-153621600	Weak transcription	Fetal Heart	heart
18	chr1:153618600-153621800	Weak transcription	Psoas Muscle	Psoas
19	chr1:153618600-153622000	Weak transcription	Fetal Brain Male	brain
20	chr1:153618600-153622400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:153618600-153631000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:153618600-153631000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:153618800-153620600	Weak transcription	Ovary	ovary
24	chr1:153618800-153621000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:153618800-153621600	Weak transcription	Stomach Mucosa	stomach
26	chr1:153618800-153621800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:153618800-153621800	Weak transcription	HSMMtube	muscle
28	chr1:153618800-153622000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:153618800-153622200	Weak transcription	Left Ventricle	heart
30	chr1:153618800-153622400	Weak transcription	Fetal Lung	lung
31	chr1:153618800-153625000	Weak transcription	Hela-S3	cervix
32	chr1:153618800-153625000	Weak transcription	HUVEC	blood vessel
33	chr1:153618800-153625200	Weak transcription	NHDF-Ad	bronchial
34	chr1:153618800-153625400	Weak transcription	NH-A	brain
35	chr1:153618800-153626400	Weak transcription	HepG2	liver
36	chr1:153618800-153630800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:153619000-153620800	Genic enhancers	Thymus	Thymus
38	chr1:153619000-153625000	Weak transcription	Colonic Mucosa	Colon
39	chr1:153619200-153622200	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:153619200-153623400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:153619200-153630800	Weak transcription	Fetal Kidney	kidney
42	chr1:153619400-153620600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:153619400-153620600	Genic enhancers	Fetal Muscle Leg	muscle
44	chr1:153619400-153621800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:153619400-153621800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:153619400-153622000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:153619400-153625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:153619400-153625200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:153619600-153620800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr1:153619600-153620800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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