Variant report

Variant	rs10875690
Chromosome Location	chr12:48154154-48154155
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr12:48154035-48154296	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr12:48154020-48154170	GM12864	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:48153014..48156848-chr12:48203481..48206772,3	K562	blood:
2	chr12:48151756..48154631-chr12:48166805..48168592,3	MCF-7	breast:
3	chr12:48151483..48157972-chr12:48164331..48169743,9	K562	blood:
4	chr12:48115323..48118041-chr12:48153022..48154829,2	MCF-7	breast:
5	chr12:48151782..48154257-chr12:48166848..48168699,2	MCF-7	breast:
6	chr12:48134835..48139182-chr12:48152118..48155732,5	MCF-7	breast:
7	chr12:48153850..48156955-chr12:48157657..48160878,3	K562	blood:
8	chr12:48097907..48100262-chr12:48151350..48154397,3	K562	blood:
9	chr12:48152241..48154431-chr12:48164400..48166889,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM106C-6	chr12:48153999-48154186	NONHSAT027943

No data

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000257433	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11168223	0.85[AMR][1000 genomes]
rs11168224	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11168227	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs11168228	0.82[CHD][hapmap]
rs11168231	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1548518	0.84[CHD][hapmap]
rs2238142	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes]
rs2239189	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs2301783	0.81[CEU][hapmap];0.90[CHD][hapmap];0.96[MEX][hapmap]
rs3815137	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4760731	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4768162	0.96[MEX][hapmap]
rs7397928	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963444	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7973677	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription 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 target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48151000-48154200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:48153000-48154400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:48153200-48154400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:48153400-48154200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:48153400-48154200	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr12:48153400-48154200	Enhancers	Stomach Mucosa	stomach
7	chr12:48153400-48156000	Weak transcription	Fetal Kidney	kidney
8	chr12:48153400-48159200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48153400-48161800	Weak transcription	Aorta	Aorta
10	chr12:48153600-48154200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr12:48153600-48154200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:48153600-48154200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:48153600-48154400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:48153600-48154400	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:48153600-48154400	Enhancers	Esophagus	oesophagus
16	chr12:48153600-48154400	Enhancers	Fetal Muscle Leg	muscle
17	chr12:48153600-48154400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr12:48153600-48155800	Weak transcription	Ovary	ovary
19	chr12:48153600-48156000	Weak transcription	Spleen	Spleen
20	chr12:48153600-48156800	Weak transcription	Left Ventricle	heart
21	chr12:48153600-48157000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:48153600-48157000	Weak transcription	Lung	lung
23	chr12:48153600-48157200	Weak transcription	Pancreas	Pancrea
24	chr12:48153600-48157200	Weak transcription	Right Atrium	heart
25	chr12:48153600-48157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:48153600-48157400	Weak transcription	Fetal Lung	lung
27	chr12:48153600-48157400	Weak transcription	GM12878-XiMat	blood
28	chr12:48153600-48159000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:48153600-48159400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:48153600-48159800	Weak transcription	Brain Germinal Matrix	brain
31	chr12:48153600-48161000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:48153600-48161200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:48153600-48161200	Weak transcription	NHDF-Ad	bronchial
34	chr12:48153600-48162000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr12:48153600-48162200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:48153600-48162800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:48153600-48166000	Weak transcription	Brain Angular Gyrus	brain
38	chr12:48153600-48166200	Weak transcription	Brain Anterior Caudate	brain
39	chr12:48153600-48166400	Weak transcription	Fetal Brain Female	brain
40	chr12:48153600-48166800	Weak transcription	Gastric	stomach
41	chr12:48153800-48154200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:48153800-48154200	Enhancers	A549	lung
43	chr12:48153800-48154200	Enhancers	Hela-S3	cervix
44	chr12:48153800-48154400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr12:48153800-48154400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:48153800-48154400	Enhancers	Colon Smooth Muscle	Colon
47	chr12:48153800-48154400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr12:48153800-48154600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:48153800-48154600	Enhancers	HUVEC	blood vessel
50	chr12:48153800-48154600	Enhancers	NHEK	skin

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