Variant report

Variant	rs1927641
Chromosome Location	chr9:16456911-16456912
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10115714	0.87[LWK][hapmap];0.85[YRI][hapmap]
rs10810565	0.89[JPT][hapmap]
rs1927619	0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs1927620	0.89[ASN][1000 genomes]
rs1927621	0.82[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs1927636	0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1927639	0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs1927640	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149162	0.80[ASN][1000 genomes]
rs2149163	0.90[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs2382802	0.89[ASN][1000 genomes]
rs2382803	0.89[ASN][1000 genomes]
rs4466492	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4961491	0.81[EUR][1000 genomes]
rs7026798	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs7035049	0.82[CHD][hapmap]
rs7043935	0.81[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7046026	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7046416	0.84[JPT][hapmap]
rs7853747	0.83[CHD][hapmap]
rs9298764	0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs9407774	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2761269	chr9:16454393-16462098	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1927641	SLC24A2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16421800-16460400	Weak transcription	Aorta	Aorta
2	chr9:16437400-16459200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:16438800-16458800	Weak transcription	HSMM	muscle
4	chr9:16446000-16458800	Weak transcription	NHLF	lung
5	chr9:16446400-16458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:16447000-16457600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:16447000-16458400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:16449200-16459200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:16451000-16458000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:16452200-16457800	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:16452200-16458600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:16453800-16457400	Weak transcription	GM12878-XiMat	blood
13	chr9:16453800-16458600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:16455800-16457800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:16456400-16458200	Enhancers	Ovary	ovary
16	chr9:16456400-16458800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:16456600-16457400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:16456600-16458000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:16456600-16461200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:16456800-16457800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:16456800-16458800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:16456800-16458800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr9:16456800-16459000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr9:16456800-16460600	Weak transcription	Placenta Amnion	Placenta Amnion

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