Variant report

Variant	rs2278891
Chromosome Location	chr8:95895702-95895703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:95895668-95895891	K562	blood:	n/a	n/a
2	POLR2A	chr8:95895467-95895814	K562	blood:	n/a	n/a
3	POLR2A	chr8:95895192-95896768	MCF-7	breast:	n/a	n/a
4	IRF1	chr8:95895542-95895763	K562	blood:	n/a	n/a
5	POLR2A	chr8:95895416-95899444	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:95890092..95892791-chr8:95893450..95895863,3	MCF-7	breast:
2	chr8:95893455..95896139-chr8:95897032..95901216,5	MCF-7	breast:
3	chr8:95894291..95896263-chr8:95907062..95909082,2	MCF-7	breast:
4	chr8:95885964..95888442-chr8:95891899..95896049,4	MCF-7	breast:
5	chr8:95856096..95858361-chr8:95893354..95895940,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272509	TF binding region
ENSG00000175305	Chromatin interaction
ENSG00000164941	Chromatin interaction
ENSG00000156170	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10091683	0.92[EUR][1000 genomes]
rs1011795	0.82[CEU][hapmap]
rs1011796	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs10956928	0.84[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs10956929	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10956930	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs10956931	0.87[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap]
rs10956932	0.84[CEU][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap]
rs11784717	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs12545596	0.84[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs12548999	0.87[JPT][hapmap]
rs12550765	0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs12677346	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12679044	0.92[CHB][hapmap]
rs2123647	0.84[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs2924477	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2945554	0.84[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs2956210	0.82[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs2956216	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3019175	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs3019182	0.90[EUR][1000 genomes]
rs4735310	0.92[EUR][1000 genomes]
rs4735312	0.94[EUR][1000 genomes]
rs4735328	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4735331	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs4735332	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs4735334	0.86[CEU][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs477653	0.87[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs535322	0.90[EUR][1000 genomes]
rs550418	0.83[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs550564	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs551270	0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61537129	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62523075	0.81[AMR][1000 genomes]
rs6471497	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs6471498	0.94[EUR][1000 genomes]
rs6471499	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6471500	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs683832	0.87[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs6983000	0.84[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6987256	0.83[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7001535	0.87[JPT][hapmap]
rs7005317	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7013163	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7015841	0.84[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs7017487	0.84[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs726816	0.84[CHB][hapmap]
rs7820818	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs7839728	0.91[EUR][1000 genomes]
rs896851	0.84[CHB][hapmap]
rs9643353	0.82[CEU][hapmap];0.83[MEX][hapmap]

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	nsv891203	chr8:95883232-95948202	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv891204	chr8:95883232-95965135	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2278891	DPY19L4	cis	brain	seeQTL
rs2278891	TP53INP1	cis	multi-tissue	Pritchard
rs2278891	SLC26A7	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95837000-95905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:95837400-95898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:95838200-95905600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:95839400-95904400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr8:95870200-95905200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr8:95870600-95905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:95873800-95898800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:95874200-95896600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr8:95874200-95897600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr8:95874200-95899000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr8:95874400-95896200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr8:95874400-95896400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr8:95874400-95902600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:95874400-95904600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr8:95874600-95896200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:95875600-95904400	Strong transcription	Fetal Thymus	thymus
17	chr8:95876000-95896200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr8:95876200-95899200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr8:95876200-95906600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr8:95876800-95899600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:95877000-95895800	Strong transcription	Adipose Nuclei	Adipose
22	chr8:95877000-95896200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:95877000-95899200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr8:95877200-95896800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr8:95879000-95898000	Weak transcription	Right Ventricle	heart
26	chr8:95879200-95906600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr8:95881200-95898000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr8:95881200-95905800	Weak transcription	Spleen	Spleen
29	chr8:95882200-95906600	Weak transcription	Gastric	stomach
30	chr8:95882800-95896200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr8:95883400-95905600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:95883600-95905600	Weak transcription	Small Intestine	intestine
33	chr8:95883800-95899200	Strong transcription	NHDF-Ad	bronchial
34	chr8:95884400-95898200	Strong transcription	Dnd41	blood
35	chr8:95885000-95896400	Strong transcription	HSMM	muscle
36	chr8:95885000-95899400	Strong transcription	K562	blood
37	chr8:95885400-95898800	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr8:95886000-95898400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr8:95886000-95905600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr8:95886000-95906400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:95886800-95899200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr8:95887200-95899200	Strong transcription	Osteobl	bone
43	chr8:95887200-95904600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr8:95887600-95906200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr8:95887800-95896600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr8:95888200-95906600	Weak transcription	Ovary	ovary
47	chr8:95888600-95899200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:95889000-95896200	Strong transcription	Brain Cingulate Gyrus	brain
49	chr8:95889800-95898800	Strong transcription	Hela-S3	cervix
50	chr8:95890000-95906200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links