Variant report

Variant	rs12925388
Chromosome Location	chr16:81616668-81616669
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81600677..81603897-chr16:81613066..81616910,4	MCF-7	breast:
2	chr16:81612341..81613994-chr16:81615649..81617151,2	K562	blood:
3	chr16:81616214..81616953-chr16:81730576..81731454,2	MCF-7	breast:
4	chr16:81476449..81480009-chr16:81614671..81617341,4	MCF-7	breast:
5	chr16:81614429..81616933-chr16:81620116..81623654,4	MCF-7	breast:
6	chr16:81613714..81617708-chr16:81617863..81620538,5	MCF-7	breast:
7	chr16:81554501..81557421-chr16:81614817..81617531,2	MCF-7	breast:
8	chr16:81477202..81480429-chr16:81614800..81620694,9	MCF-7	breast:
9	chr16:81613896..81616758-chr16:81641074..81643658,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000153815	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11640346	0.87[EUR][1000 genomes]
rs11642655	0.87[EUR][1000 genomes]
rs11644375	0.88[EUR][1000 genomes]
rs11648151	0.85[EUR][1000 genomes]
rs11649004	0.88[EUR][1000 genomes]
rs12918645	0.93[EUR][1000 genomes]
rs12923364	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12924701	0.90[EUR][1000 genomes]
rs12926649	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12929303	0.87[EUR][1000 genomes]
rs12930698	0.87[EUR][1000 genomes]
rs12930850	0.86[EUR][1000 genomes]
rs12931242	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12934751	0.89[EUR][1000 genomes]
rs4483835	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6564890	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7189295	0.84[EUR][1000 genomes]
rs7196195	0.84[EUR][1000 genomes]
rs7196548	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7198940	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7199293	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8045100	0.88[EUR][1000 genomes]
rs8045875	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9937613	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	71 gene(s)	inside rSNPs	diseases
2	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1057791	chr16:81515036-81644651	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription 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	6 gene(s)	inside rSNPs	diseases
5	nsv542993	chr16:81515036-81644651	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1062659	chr16:81547280-81668786	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1898	chr16:81581637-81626505	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81585600-81628600	Weak transcription	GM12878-XiMat	blood
2	chr16:81588200-81640800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr16:81593200-81619400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr16:81593200-81621000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr16:81593200-81622400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:81593200-81641200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:81593400-81619200	Weak transcription	K562	blood
8	chr16:81599000-81633000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:81602200-81617800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr16:81602600-81619200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr16:81603200-81617200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr16:81604200-81619200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr16:81606600-81618000	Weak transcription	Dnd41	blood
14	chr16:81606600-81619200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr16:81608000-81623400	Weak transcription	Fetal Brain Male	brain
16	chr16:81612200-81618400	Enhancers	Placenta	Placenta
17	chr16:81612600-81621400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr16:81613600-81617000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr16:81613600-81618000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr16:81613600-81618000	Enhancers	HMEC	breast
21	chr16:81613600-81620800	Enhancers	Stomach Mucosa	stomach
22	chr16:81613600-81621200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:81613800-81618000	Enhancers	Colonic Mucosa	Colon
24	chr16:81613800-81618000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr16:81614200-81617400	Enhancers	Liver	Liver
26	chr16:81614200-81618200	Genic enhancers	Fetal Intestine Small	intestine
27	chr16:81614400-81617800	Enhancers	Fetal Intestine Large	intestine
28	chr16:81614400-81618600	Enhancers	Duodenum Mucosa	Duodenum
29	chr16:81614800-81617400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr16:81614800-81617800	Genic enhancers	HepG2	liver
31	chr16:81615000-81618200	Enhancers	Placenta Amnion	Placenta Amnion
32	chr16:81615000-81618800	Enhancers	Esophagus	oesophagus
33	chr16:81615000-81619400	Enhancers	Small Intestine	intestine
34	chr16:81615200-81617200	Weak transcription	NH-A	brain
35	chr16:81615400-81616800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr16:81615400-81617400	Enhancers	Spleen	Spleen
37	chr16:81615400-81617800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr16:81615400-81618600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr16:81615600-81618400	Enhancers	Brain Substantia Nigra	brain
40	chr16:81615600-81619600	Enhancers	Lung	lung
41	chr16:81615600-81620600	Genic enhancers	NHEK	skin
42	chr16:81615800-81616800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr16:81615800-81617000	Enhancers	Right Ventricle	heart
44	chr16:81615800-81617600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr16:81615800-81618600	Strong transcription	Fetal Thymus	thymus
46	chr16:81615800-81620400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr16:81615800-81623800	Strong transcription	Primary B cells from cord blood	blood
48	chr16:81615800-81624800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr16:81616000-81616800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:81616000-81616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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