Variant report

Variant	rs13119277
Chromosome Location	chr4:10658129-10658130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10516208	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10938919	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11723092	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11723949	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11725559	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11726388	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11734917	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11737643	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933682	0.80[GIH][hapmap];0.87[TSI][hapmap]
rs12233843	0.93[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12499294	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12501252	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12509884	0.84[CEU][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13107947	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13111831	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13128842	0.98[EUR][1000 genomes]
rs13136927	0.86[ASW][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs13139842	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13143538	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17267821	0.85[CEU][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3935222	0.86[ASW][hapmap];0.85[GIH][hapmap]
rs4235336	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs4296670	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4309833	0.85[GIH][hapmap];0.85[TSI][hapmap]
rs4339204	1.00[EUR][1000 genomes]
rs61796835	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448177	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6850317	0.98[EUR][1000 genomes]
rs7677121	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
2	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
4	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
5	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
6	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
7	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers 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	58 gene(s)	inside rSNPs	diseases
8	nsv1010620	chr4:9937123-10686682	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
10	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
11	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
12	nsv593727	chr4:10397327-10694991	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv517971	chr4:10399068-10893253	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv878694	chr4:10407572-10783606	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv878697	chr4:10501373-10831866	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv829860	chr4:10598743-10764854	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13119277	HS3ST1	cis	parietal	SCAN
rs13119277	ACOX3	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10643400-10665600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:10656800-10659200	Weak transcription	Fetal Thymus	thymus
3	chr4:10657000-10658400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:10657000-10659400	Enhancers	NH-A	brain
5	chr4:10657600-10658400	Enhancers	Osteobl	bone
6	chr4:10657600-10659000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr4:10657600-10659200	Enhancers	NHEK	skin
8	chr4:10657600-10659600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:10657800-10659400	Enhancers	HMEC	breast
10	chr4:10657800-10659400	Enhancers	NHLF	lung
11	chr4:10658000-10658200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:10658000-10658200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr4:10658000-10658400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:10658000-10658400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr4:10658000-10658600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:10658000-10658800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:10658000-10658800	Enhancers	GM12878-XiMat	blood
18	chr4:10658000-10659800	Enhancers	HUVEC	blood vessel

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