Variant report

Variant	rs38517
Chromosome Location	chr7:28030486-28030487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10951189	0.82[CHD][hapmap]
rs12216542	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12671522	0.83[CHD][hapmap]
rs12671866	0.84[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs17156137	1.00[YRI][hapmap]
rs192254	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107821	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2107822	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs253310	0.84[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs38502	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38504	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38507	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38511	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs38513	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38514	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs38515	0.84[ASN][1000 genomes]
rs38516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4308621	0.80[ASN][1000 genomes]
rs66642060	0.81[ASN][1000 genomes]
rs6969285	0.82[JPT][hapmap];1.00[YRI][hapmap]

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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs38517	CPVL	cis	parietal	SCAN
rs38517	HOXA9	cis	parietal	SCAN
rs38517	TRIL	cis	parietal	SCAN
rs38517	HOXA13	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:28002800-28034600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:28006400-28031800	Weak transcription	NHDF-Ad	bronchial
3	chr7:28013400-28034200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:28015600-28032400	Weak transcription	Ovary	ovary
5	chr7:28017600-28042400	Weak transcription	Aorta	Aorta
6	chr7:28020000-28032400	Weak transcription	Primary B cells from cord blood	blood
7	chr7:28022400-28031000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:28022400-28036200	Weak transcription	Lung	lung
9	chr7:28026400-28032200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr7:28027200-28045800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:28027800-28039400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:28028200-28032800	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:28028400-28030600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:28028400-28031200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:28028600-28033000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:28029200-28031600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:28029400-28034400	Weak transcription	Osteobl	bone
18	chr7:28029800-28030800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:28030400-28030600	Enhancers	Liver	Liver
20	chr7:28030400-28031000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr7:28030400-28031200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr7:28030400-28033000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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