Variant report

Variant	rs6580689
Chromosome Location	chr12:49045831-49045832
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	chr12:49044206..49046725-chr12:49074611..49077605,2	K562	blood:

Variant related genes	Relation type
ENSG00000139620	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10747554	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10783273	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10783274	0.85[ASN][1000 genomes]
rs10783275	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783277	0.84[CEU][hapmap]
rs10783278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs10875850	0.94[ASN][1000 genomes]
rs10875852	0.99[ASN][1000 genomes]
rs10875853	0.99[ASN][1000 genomes]
rs10875861	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10875862	0.91[ASN][1000 genomes]
rs1110432	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168657	0.92[ASN][1000 genomes]
rs11168665	0.99[ASN][1000 genomes]
rs11168674	0.96[ASN][1000 genomes]
rs11168697	0.84[ASN][1000 genomes]
rs11168698	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11168702	0.81[JPT][hapmap]
rs12299955	0.87[ASN][1000 genomes]
rs12426435	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316514	0.89[ASN][1000 genomes]
rs1863541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1895995	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114320	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2162317	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2277365	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2277366	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2409085	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898087	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3209584	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35717253	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741629	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741630	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741632	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3803025	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3943899	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4113946	0.94[ASN][1000 genomes]
rs4500528	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4760735	0.94[ASN][1000 genomes]
rs4760737	0.95[ASN][1000 genomes]
rs4760739	0.90[ASN][1000 genomes]
rs4760740	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580690	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133756	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs7136021	0.83[ASN][1000 genomes]
rs7138190	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138930	0.84[CEU][hapmap]
rs7139236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299276	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304711	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7305907	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7306604	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7308699	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7314665	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954446	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7954548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs7964546	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7966065	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973824	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7974151	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7974625	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7975030	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7975821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332441	0.95[ASN][1000 genomes]
rs9634241	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9634262	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1043220	chr12:49045458-49065987	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6580689	C12orf54	cis	cerebellum	SCAN
rs6580689	WNT10B	cis	Muscle Skeletal	GTEx
rs6580689	SNORA2B	cis	cerebellum	SCAN
rs6580689	FAM186B	cis	cerebellum	SCAN
rs6580689	ADCY6	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49027600-49046600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:49030000-49047200	Weak transcription	Esophagus	oesophagus
3	chr12:49035200-49046800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:49035400-49046200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:49035400-49047000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:49035400-49047000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:49035800-49046800	Weak transcription	Gastric	stomach
8	chr12:49035800-49046800	Weak transcription	Ovary	ovary
9	chr12:49036800-49072000	Strong transcription	Liver	Liver
10	chr12:49037000-49046600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:49037000-49046800	Weak transcription	NHLF	lung
12	chr12:49037200-49046400	Weak transcription	HUVEC	blood vessel
13	chr12:49037400-49046400	Weak transcription	Brain Germinal Matrix	brain
14	chr12:49037400-49046800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:49037400-49047400	Weak transcription	Fetal Brain Male	brain
16	chr12:49037800-49056600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr12:49037800-49072400	Strong transcription	Placenta	Placenta
18	chr12:49038200-49070800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:49038400-49060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:49038800-49071800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49039000-49072200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:49039200-49046400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:49039200-49047600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:49039400-49068800	Weak transcription	Right Atrium	heart
25	chr12:49039400-49071800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:49039800-49071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:49039800-49071000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:49040000-49057000	Strong transcription	Dnd41	blood
29	chr12:49040000-49059400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:49040000-49072600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:49040200-49047800	Weak transcription	Pancreas	Pancrea
32	chr12:49040400-49047400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:49040400-49051800	Strong transcription	HSMM	muscle
34	chr12:49040400-49060600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:49040400-49072800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:49041000-49046400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:49041000-49046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:49041000-49046400	Weak transcription	Hela-S3	cervix
39	chr12:49041000-49047400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:49041000-49071800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:49041200-49061200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:49041200-49068200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr12:49041400-49047200	Weak transcription	Small Intestine	intestine
44	chr12:49041600-49065200	Weak transcription	Stomach Mucosa	stomach
45	chr12:49041800-49054400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:49041800-49065200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:49041800-49070800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:49041800-49071000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:49041800-49072400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:49041800-49073800	Strong transcription	Fetal Intestine Large	intestine

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