Variant report

Variant	rs6487233
Chromosome Location	chr12:21638570-21638571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21628982..21633807-chr12:21637504..21641052,4	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10161130	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10161132	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs10743416	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10770810	0.81[CHB][hapmap]
rs10841815	0.81[CHB][hapmap]
rs10841832	0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs10841834	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841835	0.82[CEU][hapmap]
rs10841841	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs11046055	0.81[CHB][hapmap]
rs11046064	0.81[CHB][hapmap]
rs11046065	0.90[CHB][hapmap]
rs11046078	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11608682	0.81[CHB][hapmap]
rs11610942	0.81[CHB][hapmap]
rs11612017	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12318289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12372774	0.81[CHB][hapmap]
rs12582538	0.81[CHB][hapmap]
rs13035	0.85[CHB][hapmap]
rs1366	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs1476904	0.85[CHB][hapmap]
rs1476905	0.81[CHB][hapmap]
rs1476907	0.81[CHB][hapmap]
rs2058463	0.81[CHB][hapmap]
rs2058464	0.81[CHB][hapmap]
rs2110165	0.81[CHB][hapmap]
rs2159943	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2159948	0.81[CHB][hapmap]
rs2215730	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215734	0.81[CHB][hapmap]
rs2284392	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs2417979	0.80[CHB][hapmap]
rs2417980	0.80[CHB][hapmap]
rs2417982	0.80[CHB][hapmap]
rs2417984	0.81[CHB][hapmap]
rs3213212	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3752648	0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs3759229	0.81[CHB][hapmap]
rs3825287	0.80[CHB][hapmap]
rs4762829	0.81[CHB][hapmap]
rs4762830	0.81[CHB][hapmap]
rs4762831	0.81[CHB][hapmap]
rs6487222	0.81[CHB][hapmap]
rs6487223	0.81[CHB][hapmap]
rs6487229	0.81[CHB][hapmap]
rs7134243	0.81[CHB][hapmap]
rs7135390	0.81[CHB][hapmap]
rs7136175	0.81[CHB][hapmap]
rs7137034	0.81[CHB][hapmap]
rs714357	0.81[CHB][hapmap]
rs7303408	0.81[CHB][hapmap]
rs7310953	0.81[CHB][hapmap]
rs768833	0.81[CHB][hapmap]
rs7970416	0.86[CEU][hapmap];0.80[CHB][hapmap]
rs917855	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs997820	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6487233	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs6487233	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs6487233	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs6487233	PYROXD1	cis	parietal	SCAN
rs6487233	PYROXD1	cis	lung	GTEx
rs6487233	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs6487233	PYROXD1	cis	cerebellum	SCAN
rs6487233	PYROXD1	cis	Esophagus Muscularis	GTEx
rs6487233	RECQL	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21595800-21650000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:21607000-21645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:21611000-21652800	Weak transcription	Small Intestine	intestine
4	chr12:21611000-21653600	Weak transcription	Esophagus	oesophagus
5	chr12:21611200-21640800	Weak transcription	Fetal Heart	heart
6	chr12:21614800-21652800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:21617000-21653000	Weak transcription	Colonic Mucosa	Colon
8	chr12:21619800-21652200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr12:21619800-21652400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:21619800-21652400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr12:21620200-21652600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:21620600-21652200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr12:21623200-21649400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:21623800-21639000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:21623800-21639600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:21624200-21639800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:21626600-21641000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:21628200-21649200	Weak transcription	HepG2	liver
19	chr12:21630400-21652000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:21630400-21652400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:21632000-21649000	Weak transcription	Psoas Muscle	Psoas
22	chr12:21632600-21646800	Weak transcription	Fetal Intestine Small	intestine
23	chr12:21632800-21639400	Strong transcription	NH-A	brain
24	chr12:21633600-21642000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:21633800-21641000	Weak transcription	Brain Angular Gyrus	brain
26	chr12:21633800-21641800	Weak transcription	NHEK	skin
27	chr12:21633800-21642000	Weak transcription	Brain Substantia Nigra	brain
28	chr12:21633800-21645400	Weak transcription	Gastric	stomach
29	chr12:21633800-21645600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:21633800-21645600	Weak transcription	Fetal Stomach	stomach
31	chr12:21633800-21645600	Weak transcription	Right Ventricle	heart
32	chr12:21633800-21647000	Weak transcription	Pancreas	Pancrea
33	chr12:21633800-21647000	Weak transcription	Spleen	Spleen
34	chr12:21633800-21647400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:21633800-21648600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:21634000-21642000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:21634200-21649000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:21635200-21646200	Weak transcription	Fetal Kidney	kidney
39	chr12:21635600-21641800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:21635600-21642400	Weak transcription	Lung	lung
41	chr12:21635600-21649000	Weak transcription	Aorta	Aorta
42	chr12:21635800-21645400	Weak transcription	Brain Germinal Matrix	brain
43	chr12:21635800-21645400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:21635800-21647000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:21635800-21647000	Weak transcription	Hela-S3	cervix
46	chr12:21636000-21647600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:21636000-21649600	Weak transcription	Fetal Brain Male	brain
48	chr12:21636200-21640800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:21636200-21641000	Weak transcription	Fetal Brain Female	brain
50	chr12:21636200-21641200	Weak transcription	HMEC	breast

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