Variant report

Variant	rs3098719
Chromosome Location	chr8:95541663-95541664
allele	A/C/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	SIN3AK20	chr8:95540607-95541708	MCF-7	breast:	n/a	n/a
2	NFYA	chr8:95541629-95541682	GM12878	blood:	n/a	n/a
3	GATA3	chr8:95540528-95541676	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:95540816..95542532-chr8:95731372..95733184,2	MCF-7	breast:
2	chr8:95539618..95543703-chr8:95563899..95568056,6	MCF-7	breast:
3	chr8:95536103..95541001-chr8:95541149..95546680,4	MCF-7	breast:
4	chr8:95539392..95541672-chr8:95550945..95553259,2	MCF-7	breast:

Variant related genes	Relation type
KIAA1429	TF binding region
ENSG00000254315	TF binding region
ENSG00000164944	Chromatin interaction
ENSG00000253704	Chromatin interaction
ENSG00000156162	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1023766	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372047	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1834525	0.86[ASN][1000 genomes]
rs1866845	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099788	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2119460	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2381830	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2381831	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3098707	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3098708	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3098709	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3098712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3098715	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3098716	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098718	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098725	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099403	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099404	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099406	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099407	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099412	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3099413	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3102841	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3102845	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3102851	0.84[ASN][1000 genomes]
rs3102855	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3102859	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102862	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3102874	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3102875	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3102877	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3133601	0.86[ASN][1000 genomes]
rs3133635	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3133637	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3133640	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3133645	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133648	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133649	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133651	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3133654	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3133656	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3133657	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3133658	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs957446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv611750	chr8:95519205-95574634	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95493000-95549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:95497200-95564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr8:95498400-95554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:95499400-95552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr8:95516800-95554600	Strong transcription	Fetal Thymus	thymus
6	chr8:95520400-95555200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr8:95520600-95552400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr8:95527600-95548600	Strong transcription	Fetal Muscle Leg	muscle
9	chr8:95528000-95542400	Weak transcription	Pancreas	Pancrea
10	chr8:95528400-95542400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr8:95532800-95558800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr8:95534000-95543600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr8:95534200-95545000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:95535400-95556000	Weak transcription	Fetal Heart	heart
15	chr8:95535800-95549800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:95535800-95555600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr8:95536000-95555600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:95536200-95549200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:95536400-95552200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr8:95536600-95542400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr8:95536600-95557000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr8:95536800-95543200	Strong transcription	Rectal Smooth Muscle	rectum
23	chr8:95536800-95543400	Strong transcription	Brain Germinal Matrix	brain
24	chr8:95536800-95546600	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr8:95536800-95549800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr8:95536800-95550600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr8:95536800-95551400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr8:95536800-95552400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr8:95536800-95556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:95537000-95541800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:95537000-95541800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr8:95537000-95543400	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr8:95537000-95543600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr8:95537000-95543600	Strong transcription	A549	lung
35	chr8:95537000-95544400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr8:95537000-95545200	Strong transcription	Fetal Brain Female	brain
37	chr8:95537000-95545200	Strong transcription	HepG2	liver
38	chr8:95537000-95547000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr8:95537000-95547800	Strong transcription	Brain Anterior Caudate	brain
40	chr8:95537000-95548000	Strong transcription	Thymus	Thymus
41	chr8:95537000-95548400	Strong transcription	Brain Hippocampus Middle	brain
42	chr8:95537000-95548400	Strong transcription	Hela-S3	cervix
43	chr8:95537000-95549000	Strong transcription	GM12878-XiMat	blood
44	chr8:95537000-95549400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr8:95537000-95550600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr8:95537000-95550600	Strong transcription	Fetal Lung	lung
47	chr8:95537000-95550800	Strong transcription	Dnd41	blood
48	chr8:95537000-95551000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr8:95537000-95552000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr8:95537000-95552200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links