Variant report

Variant	rs10841841
Chromosome Location	chr12:21677454-21677455
allele	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	SETDB1	chr12:21677129-21677471	U2OS	brain:	n/a	n/a
2	POLR2A	chr12:21677155-21677897	K562	blood:	n/a	n/a

Variant related genes	Relation type
C12orf39	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1048617	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10743416	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs10841834	0.88[CHD][hapmap]
rs11046101	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11610942	0.81[CEU][hapmap]
rs11612017	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs12318289	0.94[CHB][hapmap]
rs12372774	0.81[CEU][hapmap]
rs12582538	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13035	0.84[CEU][hapmap]
rs1366	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1963817	0.81[CEU][hapmap]
rs2284392	0.83[CHD][hapmap]
rs3213212	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4565955	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487233	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs7135390	0.81[CEU][hapmap]
rs7319	0.81[CEU][hapmap]
rs768833	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs997820	0.83[MEX][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10841841	FLJ22028	cis	normal skin	skin_eQTL
rs10841841	RECQL	cis	cerebellum	SCAN
rs10841841	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs10841841	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs10841841	PYROXD1	cis	Skin Sun Exposed Lower leg	GTEx
rs10841841	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs10841841	PYROXD1	cis	parietal	SCAN
rs10841841	PYROXD1	cis	cerebellum	SCAN
rs10841841	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs10841841	PYROXD1	cis	Artery Tibial	GTEx
rs10841841	PYROXD1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
2	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
3	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
6	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:21657600-21680400	Weak transcription	Gastric	stomach
8	chr12:21666000-21680200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:21666800-21679800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:21666800-21680000	Weak transcription	Psoas Muscle	Psoas
11	chr12:21666800-21680200	Weak transcription	Colonic Mucosa	Colon
12	chr12:21666800-21680400	Weak transcription	Spleen	Spleen
13	chr12:21667000-21680200	Weak transcription	Left Ventricle	heart
14	chr12:21667000-21680200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:21667000-21680200	Weak transcription	HSMMtube	muscle
16	chr12:21667200-21678000	Weak transcription	Lung	lung
17	chr12:21667200-21680000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:21667200-21680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:21667200-21680000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:21667600-21680000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:21667600-21680200	Weak transcription	NHLF	lung
22	chr12:21669200-21680000	Weak transcription	HMEC	breast
23	chr12:21669400-21678200	Weak transcription	A549	lung
24	chr12:21669400-21678800	Weak transcription	Hela-S3	cervix
25	chr12:21669400-21679000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:21669400-21680200	Weak transcription	Placenta	Placenta
27	chr12:21669800-21678000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:21669800-21679800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:21670000-21678000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:21670200-21680000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:21670600-21679600	Weak transcription	Adipose Nuclei	Adipose
32	chr12:21670800-21680000	Weak transcription	Osteobl	bone
33	chr12:21671200-21679200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:21671600-21680000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:21671600-21680000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:21671800-21680000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:21672200-21677600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:21672200-21679200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:21672400-21679800	Weak transcription	NH-A	brain
40	chr12:21672400-21680000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:21672400-21680200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:21672400-21680200	Weak transcription	HSMM	muscle
43	chr12:21672600-21679600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:21672600-21680000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:21677000-21678000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:21677400-21678200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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