Variant report

Variant	rs830121
Chromosome Location	chr12:122427161-122427162
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122398645..122400405-chr12:122425070..122427774,2	K562	blood:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1168658	0.91[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs1169076	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1169078	0.85[EUR][1000 genomes]
rs1169081	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]
rs1169083	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1169084	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]
rs1169086	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1169087	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1169089	1.00[YRI][hapmap]
rs1169091	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1177588	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1179947	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1184893	0.94[ASN][1000 genomes]
rs12578258	0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12579389	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375653	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1375654	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1375655	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1630699	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1667586	0.85[ASN][1000 genomes]
rs1678952	0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678953	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1678970	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1720030	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1720068	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs17852561	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814592	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2009257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2018749	0.83[ASN][1000 genomes]
rs2272133	1.00[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2272135	0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs2309275	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2688411	0.81[ASN][1000 genomes]
rs2922797	0.81[ASN][1000 genomes]
rs2948663	0.81[ASN][1000 genomes]
rs2948664	0.80[ASN][1000 genomes]
rs35252940	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825172	0.86[CEU][hapmap]
rs4069666	0.91[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs483416	0.91[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs55929316	0.84[ASN][1000 genomes]
rs59972569	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs658957	0.81[ASN][1000 genomes]
rs686220	0.85[ASN][1000 genomes]
rs7309105	0.86[ASW][hapmap];0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs7313748	0.86[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs745327	0.87[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.82[ASN][1000 genomes]
rs830115	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs830118	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs830121	SUDS3	cis	cerebellum	SCAN
rs830121	WDR66	cis	cerebellum	SCAN
rs830121	CCDC60	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
3	chr12:122409800-122427200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:122409800-122428400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:122409800-122428400	Weak transcription	NHEK	skin
6	chr12:122410000-122428600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:122412800-122430600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:122413200-122428800	Weak transcription	HSMMtube	muscle
9	chr12:122415200-122434800	Weak transcription	Pancreas	Pancrea
10	chr12:122415400-122428400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:122418800-122437600	Weak transcription	Spleen	Spleen
12	chr12:122419000-122427200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:122419800-122429800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:122422000-122427200	Weak transcription	GM12878-XiMat	blood
15	chr12:122422200-122429800	Weak transcription	Thymus	Thymus
16	chr12:122422800-122428200	Weak transcription	Fetal Thymus	thymus
17	chr12:122422800-122442600	Weak transcription	Fetal Kidney	kidney
18	chr12:122423000-122428400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:122425000-122428200	Weak transcription	HepG2	liver
20	chr12:122427000-122428800	Enhancers	Fetal Stomach	stomach

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