Variant report

Variant	rs10770819
Chromosome Location	chr12:21670410-21670411
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21654473..21659052-chr12:21670057..21674835,6	K562	blood:
2	chr12:21666099..21668505-chr12:21668536..21671439,2	K562	blood:
3	chr12:21659626..21662190-chr12:21669299..21671528,2	K562	blood:

Variant related genes	Relation type
ENSG00000004700	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10492117	0.84[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs10841833	0.86[CHD][hapmap]
rs10841835	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs10841836	0.84[EUR][1000 genomes]
rs10841837	0.84[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10841839	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs10841840	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs11046089	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs11046093	0.94[CHD][hapmap];0.91[MEX][hapmap]
rs11046098	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11046099	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs11046100	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs11046102	0.93[ASN][1000 genomes]
rs12231436	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs12423412	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs12582513	0.84[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12582514	0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs12822436	0.84[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs12829302	0.83[CHB][hapmap]
rs12829508	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs12833589	0.83[CHB][hapmap]
rs1366	0.83[GIH][hapmap]
rs2110159	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap]
rs2159944	0.80[CHD][hapmap]
rs2284393	0.82[CHB][hapmap];0.89[CHD][hapmap]
rs2284394	0.81[CHD][hapmap]
rs2300211	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2417991	0.84[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs3088178	0.82[AFR][1000 genomes]
rs34965831	0.84[EUR][1000 genomes]
rs35538394	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3782661	0.81[CEU][hapmap];0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs4762834	0.84[CHB][hapmap];0.92[CHD][hapmap]
rs4762835	0.84[CEU][hapmap];0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs61926331	0.86[ASN][1000 genomes]
rs61926332	0.81[ASN][1000 genomes]
rs7313618	0.83[ASW][hapmap]

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	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv528556	chr12:21664879-21680363	Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv557743	chr12:21670410-21688900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10770819	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs10770819	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs10770819	PYROXD1	cis	parietal	SCAN
rs10770819	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs10770819	PYROXD1	cis	cerebellum	SCAN
rs10770819	RECQL	cis	cerebellum	SCAN
rs10770819	LOC642732	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21655400-21674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:21656000-21671800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:21656000-21672800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:21656000-21674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:21656000-21674600	Weak transcription	Fetal Kidney	kidney
6	chr12:21656200-21671800	Weak transcription	Thymus	Thymus
7	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
8	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
9	chr12:21656800-21671400	Weak transcription	Fetal Heart	heart
10	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:21657600-21675000	Weak transcription	Small Intestine	intestine
13	chr12:21657600-21675400	Weak transcription	Fetal Brain Male	brain
14	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
15	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:21657600-21680400	Weak transcription	Gastric	stomach
17	chr12:21660000-21671600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:21660000-21672000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr12:21660200-21671600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:21660200-21672600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:21660400-21671600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:21660400-21672200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:21660600-21670800	Strong transcription	Osteobl	bone
24	chr12:21660600-21672600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:21660800-21671600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:21660800-21672400	Strong transcription	Liver	Liver
27	chr12:21661000-21670600	Strong transcription	Adipose Nuclei	Adipose
28	chr12:21661400-21670800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:21661400-21677200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:21662200-21672400	Strong transcription	HSMM	muscle
31	chr12:21663400-21671000	Strong transcription	GM12878-XiMat	blood
32	chr12:21664400-21671800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:21664600-21670600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:21664800-21671600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:21664800-21672400	Strong transcription	NH-A	brain
36	chr12:21665000-21670600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:21665200-21670800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:21665600-21670600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:21665600-21670800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr12:21665800-21672400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:21666000-21671800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:21666000-21680200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:21666800-21671600	Weak transcription	Brain Germinal Matrix	brain
44	chr12:21666800-21671600	Weak transcription	Ovary	ovary
45	chr12:21666800-21672800	Weak transcription	NHEK	skin
46	chr12:21666800-21675800	Weak transcription	HepG2	liver
47	chr12:21666800-21676800	Weak transcription	Fetal Brain Female	brain
48	chr12:21666800-21679800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:21666800-21680000	Weak transcription	Psoas Muscle	Psoas
50	chr12:21666800-21680200	Weak transcription	Colonic Mucosa	Colon

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