Variant report

Variant	rs1169084
Chromosome Location	chr12:122447128-122447129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122444926..122447764-chr12:122458397..122461144,2	K562	blood:
2	chr12:122445617..122452949-chr12:122456112..122461928,13	MCF-7	breast:
3	chr12:122445744..122449221-chr12:122451078..122453446,3	K562	blood:
4	chr12:122440790..122443569-chr12:122445704..122448468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255856	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1168658	0.91[MEX][hapmap];0.84[TSI][hapmap]
rs1169076	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1169081	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]
rs1169083	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169086	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169087	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1169089	1.00[YRI][hapmap]
rs1169091	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1177588	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1179947	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1184893	0.88[ASN][1000 genomes]
rs12578258	0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs12579389	0.80[ASN][1000 genomes]
rs1375653	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1375654	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1375655	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1630699	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1678952	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1678953	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1678970	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1720030	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1720068	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs17852561	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1814592	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009257	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2018749	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2272133	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2272135	0.82[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs2309275	0.83[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4069666	0.91[MEX][hapmap];0.84[TSI][hapmap]
rs483416	0.91[MEX][hapmap];0.84[TSI][hapmap]
rs55929316	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59972569	0.80[ASN][1000 genomes]
rs7309105	0.86[ASW][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs7313748	0.86[ASW][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs745327	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830115	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs830121	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1169084	SUDS3	cis	cerebellum	SCAN
rs1169084	WDR66	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122442600-122458800	Weak transcription	Aorta	Aorta
2	chr12:122443000-122449000	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:122443000-122458800	Weak transcription	Brain Anterior Caudate	brain
4	chr12:122443400-122458800	Weak transcription	Right Ventricle	heart
5	chr12:122443400-122459000	Weak transcription	Right Atrium	heart
6	chr12:122443600-122448400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:122444600-122458600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:122444800-122447200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:122444800-122449200	Enhancers	Fetal Thymus	thymus
10	chr12:122445000-122447800	Enhancers	Thymus	Thymus
11	chr12:122445000-122448600	Enhancers	Primary B cells from cord blood	blood
12	chr12:122446000-122447400	Enhancers	Adipose Nuclei	Adipose
13	chr12:122446000-122451400	Weak transcription	Dnd41	blood
14	chr12:122446600-122447400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr12:122446600-122447400	Enhancers	HSMMtube	muscle
16	chr12:122446600-122448200	Enhancers	GM12878-XiMat	blood
17	chr12:122446800-122447200	Enhancers	Fetal Muscle Leg	muscle
18	chr12:122446800-122447400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:122446800-122447400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr12:122446800-122447400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:122446800-122447400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr12:122446800-122447400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr12:122447000-122447200	Enhancers	Fetal Muscle Trunk	muscle
24	chr12:122447000-122448200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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