Variant report

Variant	rs16893054
Chromosome Location	chr8:124928262-124928263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:124927561..124929328-chr8:124931006..124932558,2	MCF-7	breast:
2	chr8:124920895..124922660-chr8:124926513..124928281,2	K562	blood:
3	chr8:124928038..124929759-chr8:124955238..124957453,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1007106	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs11987138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11993828	0.81[CEU][hapmap]
rs13250190	0.86[JPT][hapmap]
rs13260693	0.84[ASN][1000 genomes]
rs13268486	0.86[JPT][hapmap]
rs13268977	0.86[JPT][hapmap]
rs13277597	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs13280610	0.82[JPT][hapmap]
rs16899008	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs16899027	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs16899029	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs16899037	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16899040	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16899044	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899047	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34895349	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34943415	0.92[ASN][1000 genomes]
rs35444607	0.90[ASN][1000 genomes]
rs4242351	0.86[JPT][hapmap]
rs4285467	0.81[CEU][hapmap]
rs4285468	0.81[CEU][hapmap];0.84[CHD][hapmap]
rs4299983	0.86[JPT][hapmap]
rs4355755	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4413758	0.86[JPT][hapmap]
rs4472497	0.81[CEU][hapmap]
rs4478556	0.81[CEU][hapmap];0.84[CHD][hapmap]
rs4492357	0.86[JPT][hapmap]
rs4509302	0.86[JPT][hapmap]
rs4537289	0.81[CEU][hapmap];0.84[CHD][hapmap]
rs4587311	0.81[CEU][hapmap];0.84[CHD][hapmap]
rs4596635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4870873	0.88[ASN][1000 genomes]
rs4870874	0.87[ASN][1000 genomes]
rs4870875	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4870876	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4870879	0.80[CEU][hapmap]
rs4871417	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4871421	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4871422	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4871423	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871428	0.86[JPT][hapmap]
rs4871429	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs4871430	0.86[JPT][hapmap]
rs4871431	0.86[JPT][hapmap]
rs4871432	0.89[JPT][hapmap]
rs4871433	0.90[JPT][hapmap]
rs4871434	0.86[JPT][hapmap]
rs4871435	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs4871436	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs4871437	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs4871439	0.86[JPT][hapmap]
rs55834043	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66846856	0.82[ASN][1000 genomes]
rs6984557	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7005131	0.88[ASN][1000 genomes]
rs7464664	0.86[JPT][hapmap]
rs746745	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs746746	0.85[ASN][1000 genomes]
rs746747	0.81[CEU][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs7821233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7822699	0.89[ASN][1000 genomes]
rs7826291	0.81[CEU][hapmap]
rs7837892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838437	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs7838453	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7838473	0.86[JPT][hapmap]
rs7839327	0.86[JPT][hapmap]
rs7839570	0.89[ASN][1000 genomes]
rs7842762	0.86[CHD][hapmap];0.86[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	nsv1033617	chr8:124895516-125012783	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1035035	chr8:124895516-125020472	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv612141	chr8:124895809-125006490	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv612142	chr8:124896389-125006490	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv612143	chr8:124927711-124988267	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16893054	POU5F1B	cis	parietal	SCAN
rs16893054	TINF2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:124926800-124928600	Active TSS	Fetal Intestine Small	intestine
2	chr8:124927000-124928400	Active TSS	Fetal Stomach	stomach
3	chr8:124927000-124928800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr8:124927000-124930000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:124927000-124932600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr8:124927600-124929000	Weak transcription	Fetal Muscle Leg	muscle
7	chr8:124927600-124932800	Weak transcription	Stomach Mucosa	stomach
8	chr8:124927600-124934000	Weak transcription	HSMMtube	muscle
9	chr8:124927600-124934000	Weak transcription	K562	blood
10	chr8:124927800-124928800	Enhancers	Primary B cells from peripheral blood	blood
11	chr8:124928000-124928400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr8:124928200-124929200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr8:124928200-124931400	Weak transcription	Fetal Intestine Large	intestine

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