Variant report

Variant	rs12538893
Chromosome Location	chr7:98908497-98908498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:98667554..98669412-chr7:98906723..98909530,2	MCF-7	breast:
2	chr7:98871527..98872136-chr7:98908375..98909032,2	MCF-7	breast:
3	chr7:98899998..98902363-chr7:98908197..98910992,2	K562	blood:
4	chr7:98863715..98866247-chr7:98906796..98908535,2	K562	blood:
5	chr7:98907871..98910237-chr7:99004438..99006851,2	K562	blood:

Variant related genes	Relation type
ENSG00000106245	Chromatin interaction
ENSG00000002079	Chromatin interaction
ENSG00000106244	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10279308	0.81[CEU][hapmap]
rs11771702	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11974885	0.80[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11976700	0.89[ASN][1000 genomes]
rs11977673	1.00[CHB][hapmap]
rs11978089	0.83[CEU][hapmap]
rs12112936	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12113440	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17161662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161695	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2003499	0.81[CEU][hapmap]
rs4729532	0.81[CEU][hapmap]
rs59131705	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6651108	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs68164591	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955490	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6957987	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6958704	1.00[ASN][1000 genomes]
rs6973408	1.00[ASN][1000 genomes]
rs73395508	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733991	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9969217	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9969386	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
rs12538893	GS1-259H13.2	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98903800-98910400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:98906400-98910200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:98906800-98908600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr7:98906800-98912000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:98907200-98910400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:98907400-98909200	Weak transcription	Stomach Mucosa	stomach
7	chr7:98908000-98917800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:98908200-98910000	Weak transcription	A549	lung
9	chr7:98908200-98922600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:98908400-98909200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr7:98908400-98910000	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:98908400-98921800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:98908400-98923000	Weak transcription	Aorta	Aorta

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