Variant report

Variant	rs1169081
Chromosome Location	chr12:122405912-122405913
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122399290..122403037-chr12:122405786..122408622,3	K562	blood:
2	chr12:122396876..122400542-chr12:122404615..122407753,3	MCF-7	breast:
3	chr12:122403298..122406654-chr12:122407062..122410131,3	K562	blood:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1168658	0.95[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1169076	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1169078	0.83[EUR][1000 genomes]
rs1169079	0.85[ASN][1000 genomes]
rs1169083	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1169084	0.87[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1169086	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1169087	0.88[ASN][1000 genomes]
rs1169089	0.88[YRI][hapmap]
rs1169091	0.87[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1177588	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1177589	0.85[ASN][1000 genomes]
rs1179947	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1184893	0.99[ASN][1000 genomes]
rs12578258	0.87[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12579389	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1375653	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1375654	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1375655	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs14259	0.80[EUR][1000 genomes]
rs1630699	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1667586	0.91[ASN][1000 genomes]
rs1678952	0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1678953	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1678970	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1720030	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1720068	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17852561	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1814592	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2009257	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2272133	0.95[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap]
rs2272135	0.87[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs2309275	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2442439	0.81[EUR][1000 genomes]
rs2688409	0.81[EUR][1000 genomes]
rs2688411	0.86[ASN][1000 genomes]
rs2922797	0.87[ASN][1000 genomes]
rs2948663	0.87[ASN][1000 genomes]
rs2948664	0.85[ASN][1000 genomes]
rs35252940	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3825172	0.91[CEU][hapmap]
rs4069666	0.95[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs483416	0.95[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs508395	0.80[EUR][1000 genomes]
rs59972569	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs658957	0.86[ASN][1000 genomes]
rs686220	0.91[ASN][1000 genomes]
rs7309105	0.95[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap]
rs7313748	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs745327	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs830115	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830118	0.86[ASN][1000 genomes]
rs830121	0.87[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs876934	0.80[EUR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1169081	SUDS3	cis	cerebellum	SCAN
rs1169081	WDR66	cis	cerebellum	SCAN
rs1169081	CCDC60	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
2	chr12:122375800-122415800	Weak transcription	Liver	Liver
3	chr12:122376000-122413000	Weak transcription	Aorta	Aorta
4	chr12:122377400-122406200	Weak transcription	Thymus	Thymus
5	chr12:122391400-122410800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:122391800-122410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:122394200-122407600	Weak transcription	Brain Angular Gyrus	brain
9	chr12:122394200-122411000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:122394200-122411200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:122396000-122408000	Weak transcription	Fetal Intestine Small	intestine
12	chr12:122396600-122408200	Weak transcription	Fetal Brain Female	brain
13	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
14	chr12:122396800-122410800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:122397200-122406000	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:122397200-122408400	Weak transcription	Brain Substantia Nigra	brain
17	chr12:122397600-122406000	Weak transcription	Esophagus	oesophagus
18	chr12:122398800-122406200	Weak transcription	Fetal Thymus	thymus
19	chr12:122399000-122411000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:122399000-122411000	Weak transcription	Gastric	stomach
21	chr12:122400200-122408200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:122401400-122408200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:122402000-122406000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:122402000-122408800	Weak transcription	Pancreas	Pancrea
25	chr12:122402000-122412400	Weak transcription	Ovary	ovary
26	chr12:122402000-122412800	Weak transcription	Spleen	Spleen
27	chr12:122402800-122407200	Weak transcription	Placenta	Placenta
28	chr12:122403000-122408400	Weak transcription	NH-A	brain
29	chr12:122403400-122406800	Weak transcription	Fetal Lung	lung
30	chr12:122403400-122407600	Weak transcription	A549	lung
31	chr12:122403400-122410800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:122403400-122411000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:122403400-122417200	Weak transcription	NHDF-Ad	bronchial
34	chr12:122403600-122407800	Weak transcription	HUVEC	blood vessel
35	chr12:122403600-122408200	Weak transcription	Fetal Kidney	kidney
36	chr12:122403800-122412400	Weak transcription	HSMM	muscle
37	chr12:122403800-122412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:122404000-122406000	Weak transcription	Osteobl	bone
39	chr12:122404000-122406400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:122404000-122410000	Weak transcription	HMEC	breast
41	chr12:122404000-122410800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:122404000-122412400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:122404200-122406000	Weak transcription	Right Atrium	heart
44	chr12:122404600-122409800	Strong transcription	NHEK	skin
45	chr12:122404800-122406200	Strong transcription	K562	blood
46	chr12:122404800-122408600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:122404800-122409800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:122404800-122410000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:122404800-122410000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:122404800-122410000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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