Variant report

Variant	rs1841945
Chromosome Location	chr15:54270397-54270398
allele	A/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	chr15:54270376-54271098	H1-neurons	neurons:	n/a	n/a
2	CHD2	chr15:54270395-54270817	GM12878	blood:	n/a	n/a
3	MAX	chr15:54270385-54271032	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr15:54270380-54270530	HEK293	kidney:	n/a	n/a
5	RAD21	chr15:54270386-54270734	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD1	chr15:54270369-54270604	GM12878	blood:	n/a	n/a
7	CTCF	chr15:54270391-54270734	GM12878	blood:	n/a	n/a
8	ZNF263	chr15:54270308-54270917	HEK293-T-REx	kidney:	n/a	n/a
9	MAX	chr15:54270353-54270885	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr15:54270300-54270450	HRE	kidney:	n/a	n/a
11	RAD21	chr15:54270322-54270846	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000259669	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10518746	0.89[JPT][hapmap]
rs12438938	0.94[JPT][hapmap]
rs12439761	0.94[JPT][hapmap]
rs1478175	0.80[EUR][1000 genomes]
rs17731753	0.88[JPT][hapmap]
rs1841946	0.96[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2061747	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2243799	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2251236	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2711593	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2711595	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2725585	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725586	0.88[ASW][hapmap];0.96[CEU][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2725587	0.83[EUR][1000 genomes]
rs4776199	0.85[JPT][hapmap]
rs991264	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv949528	chr15:54041154-54281981	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv833011	chr15:54226235-54421567	Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv569491	chr15:54260920-54397493	Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv904229	chr15:54267610-54340070	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1841945	SLC24A5	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54269200-54277200	Active TSS	Aorta	Aorta
2	chr15:54269400-54270400	Weak transcription	Esophagus	oesophagus
3	chr15:54269800-54274800	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr15:54270000-54270400	Flanking Active TSS	Fetal Brain Female	brain
5	chr15:54270000-54270600	Flanking Active TSS	Fetal Lung	lung
6	chr15:54270000-54270800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
7	chr15:54270000-54271600	Active TSS	Stomach Smooth Muscle	stomach
8	chr15:54270200-54270400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr15:54270200-54270400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:54270200-54270400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:54270200-54270400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr15:54270200-54270400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
13	chr15:54270200-54270400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
14	chr15:54270200-54270400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:54270200-54270400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:54270200-54270400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:54270200-54270400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:54270200-54270400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr15:54270200-54270400	Active TSS	Fetal Intestine Small	intestine
20	chr15:54270200-54270400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
21	chr15:54270200-54270400	Active TSS	Fetal Muscle Leg	muscle
22	chr15:54270200-54270400	Enhancers	Gastric	stomach
23	chr15:54270200-54270400	Enhancers	Ovary	ovary
24	chr15:54270200-54270400	Enhancers	Pancreas	Pancrea
25	chr15:54270200-54270400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr15:54270200-54270400	Active TSS	Rectal Smooth Muscle	rectum
27	chr15:54270200-54270400	Active TSS	A549	lung
28	chr15:54270200-54270600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:54270200-54270600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:54270200-54270600	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr15:54270200-54270600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
32	chr15:54270200-54270600	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr15:54270200-54270600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr15:54270200-54270600	Flanking Active TSS	Fetal Brain Male	brain
35	chr15:54270200-54270800	Active TSS	Brain Substantia Nigra	brain
36	chr15:54270200-54270800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr15:54270200-54271000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:54270200-54271000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
39	chr15:54270200-54271000	Bivalent/Poised TSS	HepG2	liver
40	chr15:54270200-54271200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr15:54270200-54271200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr15:54270200-54271200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:54270200-54271400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
44	chr15:54270200-54271400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr15:54270200-54271400	Active TSS	Colon Smooth Muscle	Colon
46	chr15:54270200-54271400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
47	chr15:54270200-54271600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
48	chr15:54270200-54271800	Active TSS	Brain Angular Gyrus	brain
49	chr15:54270200-54273200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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