Variant report

Variant	rs4306326
Chromosome Location	chr12:21609280-21609281
allele	A/C
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	POLR2A	chr12:21608656-21609746	HepG2	liver:	n/a	n/a
2	MYC	chr12:21609185-21609857	NB4	blood:	n/a	n/a
3	EBF1	chr12:21609212-21609451	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PYROXD1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1029931	0.81[AMR][1000 genomes]
rs12424924	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17682462	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159944	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2192177	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61926295	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61927853	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4306326	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs4306326	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs4306326	RECQL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21591800-21611000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr12:21591800-21614600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:21591800-21614800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:21591800-21621000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:21591800-21624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:21592000-21614200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:21592000-21620600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:21592000-21631000	Weak transcription	Psoas Muscle	Psoas
9	chr12:21592400-21610400	Weak transcription	NHEK	skin
10	chr12:21592800-21631400	Weak transcription	K562	blood
11	chr12:21593400-21617800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr12:21594000-21617600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:21594800-21613200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:21595600-21626200	Weak transcription	Right Ventricle	heart
15	chr12:21595800-21610400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:21595800-21611000	Weak transcription	HepG2	liver
17	chr12:21595800-21624400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:21595800-21631400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:21595800-21632600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:21595800-21633200	Weak transcription	Gastric	stomach
21	chr12:21595800-21650000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:21596000-21611800	Weak transcription	Aorta	Aorta
23	chr12:21596000-21631600	Weak transcription	Pancreas	Pancrea
24	chr12:21596200-21625000	Weak transcription	NHLF	lung
25	chr12:21597000-21617800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:21597400-21636000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:21598000-21620000	Weak transcription	A549	lung
28	chr12:21598200-21617800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:21598400-21617800	Strong transcription	Adipose Nuclei	Adipose
30	chr12:21598600-21617600	Strong transcription	Primary B cells from cord blood	blood
31	chr12:21599000-21624400	Weak transcription	Fetal Brain Male	brain
32	chr12:21599000-21629600	Weak transcription	Stomach Mucosa	stomach
33	chr12:21599200-21614400	Weak transcription	HUVEC	blood vessel
34	chr12:21599600-21609400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:21600000-21624400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:21600400-21624400	Weak transcription	Fetal Kidney	kidney
37	chr12:21601200-21609400	Weak transcription	Fetal Stomach	stomach
38	chr12:21601200-21609400	Weak transcription	Ovary	ovary
39	chr12:21601200-21609800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:21601200-21610200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:21601200-21610400	Weak transcription	Fetal Intestine Small	intestine
42	chr12:21601200-21610400	Weak transcription	Left Ventricle	heart
43	chr12:21601400-21610200	Weak transcription	Esophagus	oesophagus
44	chr12:21601400-21610600	Weak transcription	Spleen	Spleen
45	chr12:21602600-21617600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:21603800-21612600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr12:21603800-21613200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:21605600-21609600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr12:21606000-21612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:21606400-21609400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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