Variant report

Variant	rs12112936
Chromosome Location	chr7:98899500-98899501
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	chr7:98899191..98901926-chr7:98970485..98972382,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10155966	0.83[CEU][hapmap]
rs10225529	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10243678	0.83[CEU][hapmap]
rs10258757	0.83[CEU][hapmap]
rs10267346	0.86[EUR][1000 genomes]
rs10270459	0.84[CEU][hapmap]
rs10270917	0.83[CEU][hapmap]
rs10272998	0.83[CEU][hapmap]
rs10279308	0.91[CEU][hapmap]
rs11762273	0.83[CEU][hapmap]
rs11771702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972017	0.82[AMR][1000 genomes]
rs11974885	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11976700	0.89[ASN][1000 genomes]
rs11977673	1.00[CHB][hapmap]
rs11978089	0.91[CEU][hapmap]
rs12113440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538893	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17161662	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17161669	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17161695	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2003499	0.91[CEU][hapmap]
rs2072181	0.83[CEU][hapmap]
rs2286162	0.84[CEU][hapmap]
rs3801288	0.83[CEU][hapmap]
rs4729532	0.91[CEU][hapmap]
rs59131705	0.90[ASN][1000 genomes]
rs6651108	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs68164591	1.00[ASN][1000 genomes]
rs6943920	0.84[CEU][hapmap]
rs6955401	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6955490	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6957987	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958704	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973408	0.83[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73395508	1.00[ASN][1000 genomes]
rs733991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9768020	0.86[EUR][1000 genomes]
rs9969217	0.80[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9969386	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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 target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12112936	GS1-259H13.2	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98873200-98905800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:98874800-98906800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:98890800-98905800	Weak transcription	Pancreas	Pancrea
4	chr7:98893200-98906600	Weak transcription	Fetal Intestine Small	intestine
5	chr7:98893800-98906000	Weak transcription	HMEC	breast
6	chr7:98897200-98903200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:98899200-98907800	Weak transcription	Aorta	Aorta
8	chr7:98899400-98899600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:98899400-98901800	Weak transcription	Gastric	stomach
10	chr7:98899400-98907000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:98899400-98907200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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