Variant report

Variant	rs13228258
Chromosome Location	chr7:102914478-102914479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11489600	0.83[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs11772383	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12667428	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12705114	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12705115	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13221892	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13232414	0.93[ASN][1000 genomes]
rs2074624	0.91[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3959214	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4729905	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4729907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs4729909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs62480135	0.82[AMR][1000 genomes];0.86[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	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
2	nsv831084	chr7:102778908-102964970	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1794417	chr7:102814101-102928545	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv981567	chr7:102850992-102924834	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13228258	RP11-401L13.5	cis	Thyroid	GTEx
rs13228258	LRRC17	cis	parietal	SCAN
rs13228258	MOGAT3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102907400-102919400	Weak transcription	Fetal Brain Male	brain
2	chr7:102907800-102919600	Weak transcription	Fetal Thymus	thymus
3	chr7:102907800-102920000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr7:102908000-102915800	Weak transcription	Dnd41	blood
5	chr7:102909400-102920200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:102910600-102919600	Weak transcription	Fetal Stomach	stomach
7	chr7:102912800-102915000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:102912800-102918800	Weak transcription	Fetal Brain Female	brain
9	chr7:102913000-102919600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:102913000-102920000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:102913200-102914800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:102914200-102915200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:102914200-102915800	Weak transcription	GM12878-XiMat	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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