Variant report

Variant	rs10841839
Chromosome Location	chr12:21673363-21673364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21671832..21674785-chr12:21687913..21690095,2	K562	blood:
2	chr12:21654473..21659052-chr12:21670057..21674835,6	K562	blood:
3	chr12:21667585..21669254-chr12:21672387..21674128,2	K562	blood:

Variant related genes	Relation type
ENSG00000004700	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1029931	0.82[CEU][hapmap]
rs10492117	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs10770819	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs10841833	1.00[ASW][hapmap];0.87[CEU][hapmap];0.82[GIH][hapmap]
rs10841835	0.83[CHB][hapmap]
rs10841837	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs10841840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046089	0.85[CHB][hapmap];0.86[CHD][hapmap];0.81[EUR][1000 genomes]
rs11046093	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs11046098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11046099	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11046100	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11046102	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12231436	0.83[CHB][hapmap];0.82[GIH][hapmap]
rs12423412	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs12424924	0.81[CEU][hapmap]
rs12582513	0.85[CHB][hapmap]
rs12582514	0.83[CHD][hapmap]
rs12822436	0.85[CHB][hapmap]
rs12829302	0.83[CHB][hapmap]
rs12829508	0.83[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12833589	0.94[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs17682462	0.80[CEU][hapmap]
rs2110159	0.83[CHB][hapmap]
rs2159944	0.87[CEU][hapmap]
rs2284393	0.82[CEU][hapmap];0.83[CHB][hapmap];0.84[TSI][hapmap]
rs2300211	0.82[CHB][hapmap]
rs2417991	0.85[CHB][hapmap]
rs3782661	0.85[CHB][hapmap]
rs4762834	0.85[CHB][hapmap];0.86[CHD][hapmap];0.81[EUR][1000 genomes]
rs4762835	0.84[CHB][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10841839	PYROXD1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21655400-21674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:21656000-21674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:21656000-21674600	Weak transcription	Fetal Kidney	kidney
4	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
5	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
6	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:21657600-21675000	Weak transcription	Small Intestine	intestine
9	chr12:21657600-21675400	Weak transcription	Fetal Brain Male	brain
10	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
11	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:21657600-21680400	Weak transcription	Gastric	stomach
13	chr12:21661400-21677200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:21666000-21680200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:21666800-21675800	Weak transcription	HepG2	liver
16	chr12:21666800-21676800	Weak transcription	Fetal Brain Female	brain
17	chr12:21666800-21679800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:21666800-21680000	Weak transcription	Psoas Muscle	Psoas
19	chr12:21666800-21680200	Weak transcription	Colonic Mucosa	Colon
20	chr12:21666800-21680400	Weak transcription	Spleen	Spleen
21	chr12:21667000-21674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:21667000-21674400	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:21667000-21675000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:21667000-21680200	Weak transcription	Left Ventricle	heart
25	chr12:21667000-21680200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:21667000-21680200	Weak transcription	HSMMtube	muscle
27	chr12:21667200-21678000	Weak transcription	Lung	lung
28	chr12:21667200-21680000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:21667200-21680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:21667200-21680000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:21667600-21680000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:21667600-21680200	Weak transcription	NHLF	lung
33	chr12:21667800-21673400	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:21669200-21675400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:21669200-21680000	Weak transcription	HMEC	breast
36	chr12:21669400-21675800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:21669400-21678200	Weak transcription	A549	lung
38	chr12:21669400-21678800	Weak transcription	Hela-S3	cervix
39	chr12:21669400-21679000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:21669400-21680200	Weak transcription	Placenta	Placenta
41	chr12:21669600-21674000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:21669600-21675000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:21669600-21676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:21669800-21673400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:21669800-21674200	Weak transcription	K562	blood
46	chr12:21669800-21678000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:21669800-21679800	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:21670000-21673600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:21670000-21675600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:21670000-21676600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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