Variant report

Variant	rs669
Chromosome Location	chr12:9232268-9232269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9218102..9220634-chr12:9230847..9232385,2	MCF-7	breast:
2	chr12:9217368..9219260-chr12:9231116..9232659,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214851	Chromatin interaction
ENSG00000245105	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10743598	0.93[CHD][hapmap]
rs10771307	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10771309	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771310	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842789	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842795	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842820	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842845	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842898	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11048789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs113973	0.93[CHD][hapmap]
rs1805651	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805652	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805653	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805654	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805655	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805658	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805659	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805660	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805662	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs1805663	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs1805664	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805666	0.80[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805667	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805678	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193005	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226379	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs226380	0.93[CHD][hapmap]
rs226383	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs226384	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs226386	0.93[CHD][hapmap]
rs226388	1.00[CHD][hapmap]
rs226389	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs226393	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs226395	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs226408	0.93[CHD][hapmap]
rs2300147	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300148	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377682	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487574	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487581	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487585	0.90[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487587	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135781	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299282	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299600	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7309361	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310089	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310167	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310884	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310921	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7955940	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7965184	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7968640	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976461	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs881376	1.00[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs669	C12orf59	cis	cerebellum	SCAN
rs669	CLECL1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9217800-9234200	Weak transcription	Primary T cells from cord blood	blood
2	chr12:9218000-9234000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:9218200-9236200	Weak transcription	Psoas Muscle	Psoas
4	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
5	chr12:9218400-9234400	Weak transcription	Right Atrium	heart
6	chr12:9218400-9236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:9218400-9236600	Weak transcription	Brain Substantia Nigra	brain
8	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:9218600-9235600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:9218600-9235800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:9218600-9236400	Weak transcription	Brain Angular Gyrus	brain
12	chr12:9218800-9236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:9218800-9236200	Weak transcription	Fetal Heart	heart
14	chr12:9219000-9233200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:9219200-9234600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
17	chr12:9219400-9233200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:9219800-9233200	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:9219800-9235800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:9220600-9232600	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:9220800-9232400	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:9222600-9232600	Strong transcription	Fetal Lung	lung
23	chr12:9222600-9233400	Strong transcription	Left Ventricle	heart
24	chr12:9224200-9232800	Strong transcription	Right Ventricle	heart
25	chr12:9225600-9233200	Strong transcription	Adipose Nuclei	Adipose
26	chr12:9225600-9236200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:9226200-9233200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:9227200-9234400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:9227400-9234200	Strong transcription	HepG2	liver
30	chr12:9228000-9234200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:9228600-9232800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:9229200-9232400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:9229200-9232800	Strong transcription	Ovary	ovary
34	chr12:9229200-9233200	Strong transcription	Aorta	Aorta
35	chr12:9229600-9234800	Weak transcription	Brain Anterior Caudate	brain
36	chr12:9230600-9232600	Strong transcription	Liver	Liver
37	chr12:9230600-9234200	Weak transcription	Lung	lung
38	chr12:9230600-9234200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:9230600-9234400	Weak transcription	Fetal Stomach	stomach
40	chr12:9230800-9240400	Weak transcription	Placenta	Placenta
41	chr12:9230800-9243600	Weak transcription	Colonic Mucosa	Colon
42	chr12:9231000-9234200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:9231000-9234400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:9231000-9235000	Weak transcription	Spleen	Spleen
45	chr12:9231200-9232600	Strong transcription	Colon Smooth Muscle	Colon
46	chr12:9231400-9232400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:9231400-9232400	Strong transcription	Rectal Smooth Muscle	rectum
48	chr12:9231800-9233000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:9232000-9236000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:9232200-9232400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum

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