Variant report

Variant	rs2278676
Chromosome Location	chr10:49718018-49718019
allele	C/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:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:49714827..49719872-chr10:49861427..49864767,4	K562	blood:
2	chr10:49715021..49718761-chr10:49720982..49725227,3	K562	blood:
3	chr10:49579606..49581410-chr10:49715776..49718367,2	K562	blood:
4	chr10:49652272..49653208-chr10:49717878..49718849,3	MCF-7	breast:
5	chr10:49676784..49678693-chr10:49717036..49719541,2	K562	blood:
6	chr10:49714562..49719396-chr10:49719920..49724610,6	K562	blood:
7	chr10:49516511..49518164-chr10:49717889..49719391,2	K562	blood:
8	chr10:49571319..49572300-chr10:49717652..49718657,4	MCF-7	breast:
9	chr10:49516068..49518164-chr10:49716922..49719391,2	K562	blood:
10	chr10:49716373..49718615-chr10:49727056..49729940,2	MCF-7	breast:
11	chr10:49571307..49572098-chr10:49717849..49718757,3	MCF-7	breast:
12	chr10:49715470..49718862-chr10:49725582..49728629,3	K562	blood:
13	chr10:49714746..49717330-chr10:49717821..49719600,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FRMPD2-1	chr10:49717904-49719721	NONHSAT013273

No data

Variant related genes	Relation type
ENSG00000107643	Chromatin interaction
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10776611	0.95[JPT][hapmap]
rs10776612	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs11101344	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11101345	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11101348	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.86[ASN][1000 genomes]
rs11101349	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11101350	0.84[ASN][1000 genomes]
rs11101351	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11101352	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11101353	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12220948	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12763969	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12768718	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12777004	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4012792	0.89[JPT][hapmap]
rs4838413	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4838414	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4838415	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4838416	0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4838608	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4838609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4838610	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4838616	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs6537563	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537564	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537565	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7093185	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7098760	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7895625	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7896115	0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7898936	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7910327	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935273	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467191	chr10:49669142-49735563	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv550813	chr10:49669142-49735563	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv550814	chr10:49705142-49735563	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv516006	chr10:49707942-49723300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2278676	PTAFR	trans	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49698000-49731200	Weak transcription	Aorta	Aorta
2	chr10:49702400-49718200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:49706000-49723400	Weak transcription	NH-A	brain
4	chr10:49709200-49720600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr10:49710000-49718600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:49710600-49718600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:49710600-49719200	Weak transcription	Pancreas	Pancrea
8	chr10:49711800-49718400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:49713000-49719200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:49714000-49727200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:49715400-49718200	Enhancers	HUVEC	blood vessel
12	chr10:49715800-49727800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:49716200-49718400	Enhancers	Right Ventricle	heart
14	chr10:49716200-49718800	Enhancers	Primary hematopoietic stem cells	blood
15	chr10:49716600-49718400	Enhancers	Brain Hippocampus Middle	brain
16	chr10:49716600-49718400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr10:49716600-49719200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr10:49716800-49718200	Enhancers	Fetal Heart	heart
19	chr10:49716800-49718400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr10:49716800-49721400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:49717000-49718400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr10:49717000-49719800	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr10:49717200-49718400	Weak transcription	Osteobl	bone
24	chr10:49717200-49719200	Strong transcription	NHLF	lung
25	chr10:49717200-49719800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:49717200-49719800	Weak transcription	Brain Anterior Caudate	brain
27	chr10:49717200-49721400	Weak transcription	HSMM	muscle
28	chr10:49717400-49719000	Weak transcription	NHDF-Ad	bronchial
29	chr10:49717400-49719400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr10:49717400-49719400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr10:49717400-49719400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr10:49717400-49719800	Weak transcription	K562	blood
33	chr10:49717400-49721000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:49717400-49721200	Weak transcription	HMEC	breast
35	chr10:49717400-49726200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr10:49717600-49719600	Weak transcription	Adipose Nuclei	Adipose
37	chr10:49717800-49718600	Weak transcription	Fetal Stomach	stomach
38	chr10:49717800-49719200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr10:49717800-49719200	Weak transcription	Spleen	Spleen
40	chr10:49717800-49720400	Weak transcription	HSMMtube	muscle
41	chr10:49718000-49718200	Enhancers	Fetal Thymus	thymus
42	chr10:49718000-49719000	Weak transcription	Brain Substantia Nigra	brain
43	chr10:49718000-49719800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr10:49718000-49720000	Weak transcription	Fetal Muscle Leg	muscle

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