Variant report

Variant	rs1561304
Chromosome Location	chr15:93259294-93259295
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr15:93258893-93259470	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr15:93258929-93259605	ECC-1	luminal epithelium:	n/a	chr15:93259010-93259024
3	NFIC	chr15:93258779-93259573	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr15:93258922-93259465	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr15:93259220-93259370	HCPEpiC	choroid plexus:	n/a	n/a
6	TEAD4	chr15:93258942-93259490	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:93258735..93260288-chr15:93446495..93448573,2	K562	blood:
2	chr15:93258240..93259897-chr15:93272535..93274240,2	MCF-7	breast:
3	chr15:93237881..93239746-chr15:93257502..93259973,2	MCF-7	breast:
4	chr15:93191617..93195403-chr15:93257490..93261490,4	MCF-7	breast:
5	chr15:93195935..93200377-chr15:93256556..93260471,5	MCF-7	breast:
6	chr15:93252649..93254753-chr15:93257319..93260184,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000240484	TF binding region
ENSG00000173575	Chromatin interaction
ENSG00000264173	Chromatin interaction
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1004309	0.99[ASN][1000 genomes]
rs12439654	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12440201	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12440617	0.87[ASN][1000 genomes]
rs12442362	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442555	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12906973	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17648050	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1808818	0.86[ASN][1000 genomes]
rs2278519	0.93[ASN][1000 genomes]
rs2278520	0.99[ASN][1000 genomes]
rs2278521	0.99[ASN][1000 genomes]
rs2387911	0.88[ASN][1000 genomes]
rs34188575	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34327113	0.91[AMR][1000 genomes]
rs34913881	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35017636	0.81[EUR][1000 genomes]
rs35095971	0.93[ASN][1000 genomes]
rs35277112	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35351684	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35663415	0.94[ASN][1000 genomes]
rs35839849	0.92[AMR][1000 genomes]
rs35982819	0.94[ASN][1000 genomes]
rs35984805	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4777729	0.91[AMR][1000 genomes]
rs4777730	0.92[AMR][1000 genomes]
rs4777731	0.89[ASN][1000 genomes]
rs4778033	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58894958	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66824972	0.86[ASN][1000 genomes]
rs66934257	0.89[AMR][1000 genomes]
rs67759391	0.92[AMR][1000 genomes]
rs67770259	0.95[ASN][1000 genomes]
rs71412559	0.84[AMR][1000 genomes]
rs71412560	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71412561	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71412562	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71412563	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71412564	0.88[AMR][1000 genomes]
rs71412566	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71412567	0.92[AMR][1000 genomes]
rs71412570	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71412571	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7165223	0.92[ASN][1000 genomes]
rs7183236	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93258200-93259800	Enhancers	Fetal Stomach	stomach
2	chr15:93258200-93260000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:93258200-93260200	Enhancers	Fetal Lung	lung
4	chr15:93258200-93261000	Weak transcription	Right Atrium	heart
5	chr15:93258200-93277000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:93258200-93277000	Weak transcription	Left Ventricle	heart
7	chr15:93258400-93259400	Enhancers	Stomach Smooth Muscle	stomach
8	chr15:93258400-93259600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:93258400-93259800	Enhancers	Fetal Muscle Leg	muscle
10	chr15:93258400-93259800	Enhancers	NH-A	brain
11	chr15:93258400-93260200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr15:93258400-93277000	Weak transcription	Ovary	ovary
13	chr15:93258600-93259800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:93258600-93277000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:93258800-93259800	Weak transcription	Brain Substantia Nigra	brain
16	chr15:93258800-93262200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:93258800-93267400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:93258800-93277000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:93258800-93277000	Weak transcription	Fetal Brain Male	brain
20	chr15:93259000-93259600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:93259000-93260400	Enhancers	Fetal Muscle Trunk	muscle
22	chr15:93259000-93260600	Weak transcription	Fetal Kidney	kidney

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