Variant report

Variant	rs2417987
Chromosome Location	chr12:21611259-21611260
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	POLR2A	chr12:21610664-21612762	A549	lung:	n/a	n/a
2	POLR2A	chr12:21610570-21611335	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:21610503-21612519	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:21610623-21613225	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:21610462-21612857	GM12892	blood:	n/a	n/a
6	MAFK	chr12:21611240-21611440	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:21610390-21612309	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21610148..21613025-chr12:21615165..21617606,4	K562	blood:

Variant related genes	Relation type
PYROXD1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1024734	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11046040	0.81[ASN][1000 genomes]
rs11046044	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11835956	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12422251	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12423173	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12423381	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423536	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12424852	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12426100	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12426103	0.81[AMR][1000 genomes]
rs12817513	0.82[ASN][1000 genomes]
rs12818516	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12826040	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1860948	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2110164	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4539382	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4762826	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131809	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7133131	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7133853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7138089	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7298136	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7310391	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7314131	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs738027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957415	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7959893	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971245	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7973116	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974817	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9668302	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2417987	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs2417987	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2417987	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs2417987	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs2417987	PYROXD1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21591800-21614600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:21591800-21614800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:21591800-21621000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:21591800-21624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:21592000-21614200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:21592000-21620600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:21592000-21631000	Weak transcription	Psoas Muscle	Psoas
8	chr12:21592800-21631400	Weak transcription	K562	blood
9	chr12:21593400-21617800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr12:21594000-21617600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:21594800-21613200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:21595600-21626200	Weak transcription	Right Ventricle	heart
13	chr12:21595800-21624400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:21595800-21631400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:21595800-21632600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:21595800-21633200	Weak transcription	Gastric	stomach
17	chr12:21595800-21650000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:21596000-21611800	Weak transcription	Aorta	Aorta
19	chr12:21596000-21631600	Weak transcription	Pancreas	Pancrea
20	chr12:21596200-21625000	Weak transcription	NHLF	lung
21	chr12:21597000-21617800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:21597400-21636000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:21598000-21620000	Weak transcription	A549	lung
24	chr12:21598200-21617800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:21598400-21617800	Strong transcription	Adipose Nuclei	Adipose
26	chr12:21598600-21617600	Strong transcription	Primary B cells from cord blood	blood
27	chr12:21599000-21624400	Weak transcription	Fetal Brain Male	brain
28	chr12:21599000-21629600	Weak transcription	Stomach Mucosa	stomach
29	chr12:21599200-21614400	Weak transcription	HUVEC	blood vessel
30	chr12:21600000-21624400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:21600400-21624400	Weak transcription	Fetal Kidney	kidney
32	chr12:21602600-21617600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:21603800-21612600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:21603800-21613200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:21606000-21612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:21606800-21613200	Strong transcription	Hela-S3	cervix
37	chr12:21607000-21645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:21607400-21617600	Strong transcription	Placenta	Placenta
39	chr12:21607600-21617600	Strong transcription	Liver	Liver
40	chr12:21608400-21618200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:21608600-21611400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr12:21608600-21612400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:21608600-21613200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:21608800-21611600	Strong transcription	HMEC	breast
45	chr12:21608800-21612000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:21608800-21612000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:21608800-21612400	Strong transcription	Fetal Brain Female	brain
48	chr12:21608800-21612800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:21609000-21612200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:21609000-21612200	Strong transcription	Brain Hippocampus Middle	brain

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