Variant report

Variant	rs10039491
Chromosome Location	chr5:177891489-177891490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177879886..177881970-chr5:177890471..177892015,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10040117	0.93[ASN][1000 genomes]
rs10043416	0.90[ASN][1000 genomes]
rs10060223	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs10069282	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479493	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11959914	1.00[JPT][hapmap]
rs12652427	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs12657817	0.87[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs1391654	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17648414	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2546626	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs2546627	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2546628	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2546629	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2546630	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2647688	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2647693	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2672819	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2672820	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2672843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2840140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4288132	0.81[EUR][1000 genomes]
rs4329031	0.88[EUR][1000 genomes]
rs4976776	1.00[JPT][hapmap]
rs4976777	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976780	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4976783	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs55662845	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56135911	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6601239	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs678011	0.95[EUR][1000 genomes]
rs6867956	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs6881003	0.87[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs7725796	0.93[EUR][1000 genomes]
rs7726272	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs952086	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv462570	chr5:177860454-178010145	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv600423	chr5:177860454-178010145	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1029822	chr5:177872333-177931889	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1033039	chr5:177873974-177926244	Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv537971	chr5:177873974-177926244	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1030915	chr5:177880081-177934927	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10039491	C2orf3	trans	cerebellum	SCAN
rs10039491	ZNF354A	cis	cerebellum	SCAN
rs10039491	ZNF354B	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177877600-177894200	Weak transcription	Spleen	Spleen
2	chr5:177877800-177895400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:177887200-177896600	Enhancers	Fetal Stomach	stomach
4	chr5:177887800-177897600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:177888000-177894400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr5:177888400-177892400	Weak transcription	Fetal Lung	lung
7	chr5:177888400-177893600	Weak transcription	Pancreas	Pancrea
8	chr5:177888600-177893400	Weak transcription	Lung	lung
9	chr5:177888600-177893800	Weak transcription	Liver	Liver
10	chr5:177888600-177894000	Weak transcription	Fetal Intestine Small	intestine
11	chr5:177888600-177894200	Weak transcription	Right Ventricle	heart
12	chr5:177888600-177895200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:177888800-177893000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:177888800-177893800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:177888800-177894200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:177889000-177893600	Weak transcription	Fetal Thymus	thymus
17	chr5:177889200-177894200	Weak transcription	Left Ventricle	heart
18	chr5:177889200-177895200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:177889400-177892200	Weak transcription	Fetal Heart	heart
20	chr5:177890000-177892200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:177890200-177893600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:177890200-177894000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:177890400-177895400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:177890600-177892200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:177890600-177892800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:177890600-177901600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:177891000-177897600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:177891200-177892200	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr5:177891200-177892600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:177891400-177892000	Enhancers	Adipose Nuclei	Adipose
31	chr5:177891400-177892400	Enhancers	NHDF-Ad	bronchial
32	chr5:177891400-177892800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr5:177891400-177894200	Weak transcription	Fetal Kidney	kidney

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