Variant report

Variant	rs2125553
Chromosome Location	chr8:113900367-113900368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1026488	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11776457	1.00[YRI][hapmap]
rs11787239	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11986076	0.84[ASN][1000 genomes]
rs13248739	0.81[ASN][1000 genomes]
rs13256271	0.86[ASN][1000 genomes]
rs13256724	0.81[ASN][1000 genomes]
rs13259225	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13259298	0.84[ASN][1000 genomes]
rs13261160	0.84[CEU][hapmap];0.80[MEX][hapmap]
rs13261301	0.88[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13264919	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13266975	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs13267779	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13272429	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13275178	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13275398	0.89[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs13276278	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1350566	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1350567	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1380134	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1380136	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1380139	1.00[ASN][1000 genomes]
rs1380140	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1380141	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs1458999	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1459000	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1459006	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459007	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs170760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1813415	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1947633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979305	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1993607	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]
rs2045540	1.00[ASN][1000 genomes]
rs2125552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2194601	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2216891	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2219486	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs231278	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs231280	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs231282	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs231283	0.84[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs231284	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs231287	0.86[ASN][1000 genomes]
rs231288	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs231301	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs231302	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs231305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs231306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs231312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs231313	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs231314	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs231315	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs231317	0.84[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs231320	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs231321	0.84[ASN][1000 genomes]
rs231322	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs231323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2446469	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2511523	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2511524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2511529	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511530	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]
rs2511536	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28830583	0.84[ASN][1000 genomes]
rs370168	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs373880	0.84[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3950980	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4028265	1.00[ASN][1000 genomes]
rs4876298	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4876499	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4876501	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7009209	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7013313	0.84[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs7818598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs958815	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2753595	chr8:113283214-114190390	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv534270	chr8:113585830-113979075	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
3	esv2754315	chr8:113736824-114048824	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv891326	chr8:113777669-114091732	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv891327	chr8:113828980-114109342	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2125553	TRMT5	trans	cerebellum	SCAN
rs2125553	CD83	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:113895400-113900400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:113895400-113904800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:113896000-113900600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr8:113896800-113905200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr8:113897000-113904800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr8:113897200-113904800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr8:113897400-113901600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr8:113897400-113905000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:113900000-113901400	Enhancers	Brain Germinal Matrix	brain
10	chr8:113900200-113900600	Flanking Active TSS	NHEK	skin
11	chr8:113900200-113900800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr8:113900200-113901200	Enhancers	Hela-S3	cervix
13	chr8:113900200-113902600	Enhancers	HMEC	breast

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