Variant report

Variant	rs12754041
Chromosome Location	chr1:180957962-180957963
allele	G/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	NFIC	chr1:180957334-180958019	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr1:180957491-180957968	ECC-1	luminal epithelium:	n/a	n/a
3	FOXA1	chr1:180957803-180958211	HepG2	liver:	n/a	n/a
4	EP300	chr1:180957354-180958096	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr1:180957526-180958019	ECC-1	luminal epithelium:	n/a	n/a
6	CEBPB	chr1:180957748-180958040	HepG2	liver:	n/a	n/a
7	NFIC	chr1:180957283-180958120	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180956077..180957992-chr1:181055022..181057950,3	K562	blood:

Variant related genes	Relation type
STX6	TF binding region
ENSG00000162783	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1044595	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10753232	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586493	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3747957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4111520	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4495657	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4652547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59145927	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6425657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6680541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7516739	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7543927	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7553330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556005	0.88[JPT][hapmap]
rs883859	0.82[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3359336	chr1:180956329-180959227	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12754041	STX6	cis	parietal	SCAN
rs12754041	RGSL1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
2	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:180939200-180965600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:180943600-180972000	Weak transcription	Psoas Muscle	Psoas
6	chr1:180943600-180979800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:180944400-180962600	Strong transcription	Osteobl	bone
8	chr1:180944800-180970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:180945400-180975000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:180945600-180974800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:180948200-180959400	Weak transcription	Stomach Mucosa	stomach
12	chr1:180948600-180961400	Strong transcription	Fetal Intestine Large	intestine
13	chr1:180948800-180959800	Strong transcription	Left Ventricle	heart
14	chr1:180948800-180961000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:180949000-180962400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:180949000-180962600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:180949400-180963800	Strong transcription	Liver	Liver
18	chr1:180949800-180962600	Strong transcription	Adipose Nuclei	Adipose
19	chr1:180949800-180962600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr1:180949800-180963800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr1:180949800-180966200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:180950000-180962600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:180950000-180964600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:180950000-180965200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:180950000-180966400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:180950000-180968200	Strong transcription	HMEC	breast
27	chr1:180950600-180962400	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr1:180950800-180962400	Strong transcription	Placenta	Placenta
29	chr1:180951400-180960200	Strong transcription	Colon Smooth Muscle	Colon
30	chr1:180951400-180966200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:180951600-180963800	Strong transcription	Fetal Lung	lung
32	chr1:180951600-180964800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:180951600-180966400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:180951800-180963600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:180952000-180963000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:180952000-180963200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:180952000-180963800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:180952000-180965200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:180952000-180966000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:180952000-180966200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:180952200-180961200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:180952200-180962200	Strong transcription	GM12878-XiMat	blood
43	chr1:180952200-180964000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:180952200-180974800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:180952400-180963800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:180952600-180966000	Strong transcription	Fetal Thymus	thymus
47	chr1:180952800-180961000	Strong transcription	Fetal Stomach	stomach
48	chr1:180952800-180966000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:180953000-180962400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr1:180953200-180959600	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links