Variant report

Variant	rs12227309
Chromosome Location	chr12:57679030-57679031
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	chr12:57673193..57675613-chr12:57676618..57679327,2	K562	blood:

Variant related genes	Relation type
ENSG00000179912	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10876968	0.92[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10876971	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876973	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876974	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172140	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172142	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172155	0.91[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11614077	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11830804	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28473132	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2943692	1.00[CEU][hapmap]
rs2943693	0.91[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap]
rs3204635	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs36050407	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs473465	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs507562	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs538548	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs567895	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6581138	0.85[EUR][1000 genomes]
rs7133572	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302906	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7966846	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7976512	1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS 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 miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12227309	OR6C1	cis	parietal	SCAN
rs12227309	RDH5	cis	cerebellum	SCAN
rs12227309	SDR9C7	cis	cerebellum	SCAN
rs12227309	ORMDL2	cis	parietal	SCAN
rs12227309	APOF	cis	parietal	SCAN
rs12227309	DNAJC14	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57654800-57705400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:57656600-57682800	Weak transcription	Fetal Brain Male	brain
3	chr12:57662800-57706000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:57667600-57685600	Weak transcription	Fetal Heart	heart
5	chr12:57667600-57687200	Weak transcription	Psoas Muscle	Psoas
6	chr12:57670200-57681400	Strong transcription	Stomach Smooth Muscle	stomach
7	chr12:57670400-57707000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:57670600-57693000	Strong transcription	Fetal Muscle Leg	muscle
9	chr12:57670600-57694400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:57670600-57698600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:57670600-57700000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr12:57671000-57681600	Strong transcription	Brain Germinal Matrix	brain
13	chr12:57671000-57694400	Strong transcription	Adipose Nuclei	Adipose
14	chr12:57671000-57700000	Strong transcription	Liver	Liver
15	chr12:57671200-57690400	Strong transcription	Fetal Brain Female	brain
16	chr12:57671600-57680400	Strong transcription	Left Ventricle	heart
17	chr12:57671600-57692200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:57672200-57688400	Weak transcription	Small Intestine	intestine
19	chr12:57672800-57688400	Weak transcription	Colonic Mucosa	Colon
20	chr12:57674200-57682800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:57674400-57684600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:57674400-57697000	Strong transcription	Placenta	Placenta
23	chr12:57674600-57682600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:57674600-57683200	Weak transcription	Right Ventricle	heart
25	chr12:57674600-57685000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:57674600-57686800	Weak transcription	Esophagus	oesophagus
27	chr12:57674600-57693200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:57674600-57693600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:57674600-57694200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:57674600-57697000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:57674600-57700000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:57674600-57702600	Weak transcription	HUVEC	blood vessel
33	chr12:57674600-57704400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:57674800-57680000	Weak transcription	NHLF	lung
35	chr12:57674800-57680400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:57674800-57681200	Weak transcription	GM12878-XiMat	blood
37	chr12:57674800-57681400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr12:57674800-57682400	Strong transcription	Primary hematopoietic stem cells	blood
39	chr12:57674800-57682800	Weak transcription	HSMMtube	muscle
40	chr12:57674800-57685600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr12:57674800-57688400	Weak transcription	NHDF-Ad	bronchial
42	chr12:57674800-57688800	Weak transcription	HMEC	breast
43	chr12:57674800-57691200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:57674800-57693600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:57674800-57694200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr12:57674800-57697400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:57674800-57697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:57674800-57700000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:57674800-57701000	Strong transcription	Primary T cells from cord blood	blood
50	chr12:57675000-57680400	Strong transcription	Primary B cells from peripheral blood	blood

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