Variant report

Variant	rs28754733
Chromosome Location	chr1:153598094-153598095
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	POLR2A	chr1:153597855-153598098	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:153598009-153598294	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153597855..153601076-chr1:153629883..153633781,4	MCF-7	breast:

Variant related genes	Relation type
S100A1	TF binding region
ENSG00000143553	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1046381	0.85[ASN][1000 genomes]
rs10797056	0.83[CHD][hapmap]
rs10797096	0.88[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs10908848	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs11265625	0.88[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11497739	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11548102	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548103	0.96[ASN][1000 genomes]
rs11548104	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11588347	0.83[EUR][1000 genomes]
rs12139953	0.82[EUR][1000 genomes]
rs12564925	0.83[CHD][hapmap]
rs12730186	0.85[EUR][1000 genomes]
rs1888115	0.83[CHD][hapmap]
rs2274739	0.83[CHD][hapmap]
rs2274740	0.83[CHD][hapmap]
rs28380060	0.83[CHD][hapmap]
rs28416529	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28518786	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28580554	0.83[CHD][hapmap]
rs35760493	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3790411	0.83[CHD][hapmap]
rs3790412	0.83[CHD][hapmap]
rs3806233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3818632	0.83[CHD][hapmap]
rs3828031	0.83[CHD][hapmap]
rs3862047	0.88[CEU][hapmap];0.83[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4072425	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4515830	0.92[CEU][hapmap]
rs4845563	0.88[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4845564	0.83[EUR][1000 genomes]
rs55772653	0.84[EUR][1000 genomes]
rs66721814	0.85[EUR][1000 genomes]
rs6674929	0.88[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7934	0.83[CHD][hapmap]
rs913861	0.80[CHD][hapmap]
rs9330298	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330299	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9330300	0.94[ASN][1000 genomes]
rs9330301	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9660679	0.94[ASN][1000 genomes]
rs9662664	0.85[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs9699949	0.96[ASN][1000 genomes]
rs9700179	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[ASN][1000 genomes]
rs9700928	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9726753	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9729773	0.98[ASN][1000 genomes]
rs9792913	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9792963	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9792967	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9793310	0.94[ASN][1000 genomes]
rs999418	0.81[EUR][1000 genomes];0.98[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs28754733	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs28754733	ZNF687	cis	cerebellum	SCAN
rs28754733	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs28754733	S100A4	cis	lymphoblastoid	seeQTL
rs28754733	S100A13	cis	parietal	SCAN
rs28754733	S100A14	cis	Esophagus Mucosa	GTEx
rs28754733	FLG	cis	cerebellum	SCAN
rs28754733	CHTOP	cis	Muscle Skeletal	GTEx
rs28754733	S100A16	cis	cerebellum	SCAN
rs28754733	SLC27A3	cis	cerebellum	SCAN
rs28754733	S100A13	cis	lymphoblastoid	seeQTL
rs28754733	S100A9	cis	parietal	SCAN
rs28754733	S100A16	cis	Muscle Skeletal	GTEx
rs28754733	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs28754733	S100A2	cis	cerebellum	SCAN
rs28754733	S100A16	cis	parietal	SCAN
rs28754733	S100A10	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153585600-153598800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:153585600-153599000	Weak transcription	Aorta	Aorta
3	chr1:153585800-153599200	Weak transcription	Fetal Brain Male	brain
4	chr1:153586000-153598800	Weak transcription	Psoas Muscle	Psoas
5	chr1:153588600-153598800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:153589200-153599400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:153589400-153598600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:153590000-153598600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:153590400-153598200	Weak transcription	Colonic Mucosa	Colon
10	chr1:153590400-153598200	Weak transcription	Pancreas	Pancrea
11	chr1:153590400-153598600	Weak transcription	Brain Anterior Caudate	brain
12	chr1:153590400-153598600	Weak transcription	Esophagus	oesophagus
13	chr1:153590400-153598600	Weak transcription	Gastric	stomach
14	chr1:153590400-153598600	Weak transcription	K562	blood
15	chr1:153590600-153598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:153590600-153599400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:153590800-153598800	Weak transcription	Stomach Mucosa	stomach
18	chr1:153591000-153598800	Strong transcription	Fetal Intestine Small	intestine
19	chr1:153592400-153598200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:153593400-153598600	Weak transcription	Fetal Lung	lung
21	chr1:153594800-153598200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:153595000-153598200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:153595000-153598400	Genic enhancers	Adipose Nuclei	Adipose
24	chr1:153595000-153598400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:153595600-153598200	Strong transcription	Fetal Intestine Large	intestine
26	chr1:153595600-153598200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:153595800-153598200	Weak transcription	A549	lung
28	chr1:153596000-153598800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:153596000-153599000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:153596200-153598400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:153596200-153598600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:153596200-153599000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:153596200-153599000	Genic enhancers	Fetal Stomach	stomach
34	chr1:153596400-153598400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:153596400-153598600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:153596400-153598800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:153596400-153598800	Enhancers	Right Ventricle	heart
38	chr1:153596600-153598800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:153596600-153598800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:153596600-153598800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:153596600-153598800	Enhancers	Fetal Heart	heart
42	chr1:153596600-153599000	Weak transcription	Fetal Thymus	thymus
43	chr1:153596800-153598200	Genic enhancers	HMEC	breast
44	chr1:153596800-153598600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:153596800-153598600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:153596800-153598600	Genic enhancers	NHEK	skin
47	chr1:153596800-153598800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:153596800-153598800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:153596800-153598800	Weak transcription	Liver	Liver
50	chr1:153596800-153598800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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