Variant report

Variant	rs16825024
Chromosome Location	chr1:186148546-186148547
allele	A/C
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	NFYA	chr1:186148429-186148619	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186148276..186150071-chr1:186151136..186154406,3	MCF-7	breast:
2	chr1:186138817..186141455-chr1:186147158..186149563,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224691	TF binding region
ENSG00000143341	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10489752	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576689	1.00[CEU][hapmap]
rs11803845	0.90[ASN][1000 genomes]
rs11808677	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809665	0.89[EUR][1000 genomes]
rs11811575	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067376	1.00[CEU][hapmap]
rs1322376	1.00[JPT][hapmap]
rs16824945	1.00[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs16825012	1.00[CEU][hapmap]
rs16825020	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs16825022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][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]
rs35594835	0.90[ASN][1000 genomes]
rs41317507	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58758627	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59091582	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59379268	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658106	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672327	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693069	0.88[TSI][hapmap]
rs6695626	1.00[CEU][hapmap]
rs72707450	0.84[EUR][1000 genomes]
rs72707466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72707470	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74136042	1.00[ASN][1000 genomes]
rs7527214	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539719	1.00[CEU][hapmap]
rs7552194	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[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	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1007237	chr1:186137724-186226502	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1009149	chr1:186147945-186206188	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186114600-186160800	Weak transcription	Fetal Kidney	kidney
2	chr1:186133600-186160800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:186134600-186152200	Weak transcription	NH-A	brain
4	chr1:186136200-186152400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:186136200-186153200	Weak transcription	Fetal Lung	lung
6	chr1:186136200-186157600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:186136800-186157000	Weak transcription	Aorta	Aorta
8	chr1:186137000-186152800	Weak transcription	Liver	Liver
9	chr1:186137200-186152000	Weak transcription	Adipose Nuclei	Adipose
10	chr1:186145000-186158400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:186145400-186151200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:186147000-186148600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:186147000-186148800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:186147000-186148800	Enhancers	HMEC	breast
15	chr1:186147200-186148600	Enhancers	NHEK	skin
16	chr1:186147800-186148600	Active TSS	Osteobl	bone
17	chr1:186147800-186148800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:186147800-186148800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:186148000-186148600	Active TSS	Right Atrium	heart
20	chr1:186148000-186148800	Active TSS	NHDF-Ad	bronchial
21	chr1:186148000-186149800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:186148000-186152200	Weak transcription	Hela-S3	cervix
23	chr1:186148000-186157000	Weak transcription	Left Ventricle	heart
24	chr1:186148200-186148600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:186148200-186148600	Active TSS	Brain Anterior Caudate	brain
26	chr1:186148200-186148600	Enhancers	Fetal Brain Female	brain
27	chr1:186148200-186148800	Enhancers	HSMM	muscle
28	chr1:186148400-186148600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr1:186148400-186148600	Enhancers	K562	blood
30	chr1:186148400-186148800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:186148400-186148800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:186148400-186148800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr1:186148400-186151400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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