Variant report

Variant	rs12113073
Chromosome Location	chr7:102482527-102482528
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	chr7:102473443..102475589-chr7:102480022..102482918,2	K562	blood:

Variant related genes	Relation type
ENSG00000252643	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10487281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11496066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12113759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17135875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135913	0.92[ASW][hapmap];1.00[CHB][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs17135916	1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs17474893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041094	1.00[CHB][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215040	0.82[TSI][hapmap]
rs2411061	1.00[CHB][hapmap]
rs3893651	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377880	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4398822	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4610658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55681588	1.00[ASN][1000 genomes]
rs55781834	1.00[ASN][1000 genomes]
rs56146438	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56186316	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56314487	1.00[ASN][1000 genomes]
rs56692051	1.00[ASN][1000 genomes]
rs6955064	1.00[ASN][1000 genomes]
rs6964296	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6968036	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs727175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192015	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192019	1.00[ASN][1000 genomes]
rs7779854	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7781557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790451	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7809047	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv608059	chr7:102470455-102504773	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12113073	CUX1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102454200-102484600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:102468000-102484600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:102470000-102490200	Weak transcription	Gastric	stomach
4	chr7:102470000-102516400	Weak transcription	Pancreas	Pancrea
5	chr7:102470400-102482800	Weak transcription	Brain Anterior Caudate	brain
6	chr7:102470800-102484400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr7:102470800-102493200	Weak transcription	Primary T cells from cord blood	blood
8	chr7:102471800-102500000	Weak transcription	Left Ventricle	heart
9	chr7:102472000-102484800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:102477800-102500800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:102478000-102489200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:102478200-102500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:102478200-102500000	Weak transcription	Ovary	ovary
14	chr7:102478800-102482800	Weak transcription	Fetal Intestine Large	intestine
15	chr7:102478800-102489600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:102478800-102492600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:102480800-102482600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr7:102480800-102482600	Enhancers	HSMM	muscle
19	chr7:102480800-102482800	Enhancers	Fetal Lung	lung
20	chr7:102481000-102483000	Enhancers	Brain Germinal Matrix	brain
21	chr7:102481000-102483000	Weak transcription	HepG2	liver
22	chr7:102481800-102482600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:102481800-102483000	Enhancers	Fetal Stomach	stomach
24	chr7:102481800-102483600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:102482000-102483400	Enhancers	NHDF-Ad	bronchial
26	chr7:102482000-102484200	Weak transcription	GM12878-XiMat	blood
27	chr7:102482000-102484600	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:102482200-102483400	Strong transcription	K562	blood
29	chr7:102482400-102483400	Enhancers	Stomach Mucosa	stomach
30	chr7:102482400-102484800	Weak transcription	HSMMtube	muscle

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