Variant report

Variant	rs12422251
Chromosome Location	chr12:21621737-21621738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1024734	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11046044	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11835956	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12423381	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12818516	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12826040	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1860948	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2417987	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4539382	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4762826	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7131809	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7133131	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7133853	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7138089	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7298136	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310391	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7314131	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs738027	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7957415	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7959893	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7971245	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7973116	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7974817	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9668302	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	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
6	nsv975459	chr12:21620789-21623981	Strong transcription Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12422251	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs12422251	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs12422251	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs12422251	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21591800-21624200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr12:21592000-21631000	Weak transcription	Psoas Muscle	Psoas
3	chr12:21592800-21631400	Weak transcription	K562	blood
4	chr12:21595600-21626200	Weak transcription	Right Ventricle	heart
5	chr12:21595800-21624400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:21595800-21631400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:21595800-21632600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:21595800-21633200	Weak transcription	Gastric	stomach
9	chr12:21595800-21650000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:21596000-21631600	Weak transcription	Pancreas	Pancrea
11	chr12:21596200-21625000	Weak transcription	NHLF	lung
12	chr12:21597400-21636000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:21599000-21624400	Weak transcription	Fetal Brain Male	brain
14	chr12:21599000-21629600	Weak transcription	Stomach Mucosa	stomach
15	chr12:21600000-21624400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:21600400-21624400	Weak transcription	Fetal Kidney	kidney
17	chr12:21607000-21645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:21610600-21626200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:21611000-21625000	Weak transcription	Brain Angular Gyrus	brain
20	chr12:21611000-21652800	Weak transcription	Small Intestine	intestine
21	chr12:21611000-21653600	Weak transcription	Esophagus	oesophagus
22	chr12:21611200-21631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:21611200-21640800	Weak transcription	Fetal Heart	heart
24	chr12:21611600-21624200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:21611800-21626600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr12:21612200-21624400	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:21612200-21630800	Weak transcription	Spleen	Spleen
28	chr12:21612400-21624400	Weak transcription	Fetal Brain Female	brain
29	chr12:21612400-21625200	Weak transcription	Aorta	Aorta
30	chr12:21612400-21627200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:21612600-21624800	Weak transcription	Brain Germinal Matrix	brain
32	chr12:21612600-21631000	Weak transcription	Lung	lung
33	chr12:21612800-21625400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:21613000-21624400	Weak transcription	Left Ventricle	heart
35	chr12:21613800-21631600	Weak transcription	Fetal Stomach	stomach
36	chr12:21614000-21625000	Weak transcription	NHEK	skin
37	chr12:21614800-21652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:21615200-21623800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:21615200-21624200	Weak transcription	HUVEC	blood vessel
40	chr12:21615600-21624400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr12:21615600-21624400	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:21616400-21624000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:21616600-21631800	Weak transcription	Fetal Intestine Small	intestine
44	chr12:21617000-21653000	Weak transcription	Colonic Mucosa	Colon
45	chr12:21617200-21624400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:21617400-21625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:21617400-21630800	Weak transcription	Thymus	Thymus
48	chr12:21617600-21624200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:21617600-21624200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:21617600-21624200	Weak transcription	Brain Cingulate Gyrus	brain

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