Variant report

Variant	rs10054931
Chromosome Location	chr5:75410511-75410512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10038280	0.97[EUR][1000 genomes]
rs10038757	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10043369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050813	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10051950	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10060618	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs10063621	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10064145	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10065114	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10067484	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs10074384	0.94[CEU][hapmap];0.91[JPT][hapmap]
rs10474460	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12513411	0.86[EUR][1000 genomes]
rs12513447	0.90[EUR][1000 genomes]
rs12656979	0.87[EUR][1000 genomes]
rs12659929	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12697846	0.87[CEU][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap]
rs13160383	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553311	0.87[EUR][1000 genomes]
rs17673786	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17746749	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1862519	0.82[CEU][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap]
rs1862520	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28554027	0.87[EUR][1000 genomes]
rs6453199	0.94[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7448740	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs767590	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7700761	0.94[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7702044	1.00[CEU][hapmap];0.81[YRI][hapmap];0.99[EUR][1000 genomes]
rs7711218	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7712198	0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7725280	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9293665	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9293666	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9293667	1.00[CEU][hapmap];0.83[JPT][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv869885	chr5:75365786-75419656	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1034853	chr5:75382047-75534981	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv462212	chr5:75388834-75534570	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv598676	chr5:75388834-75534570	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv2755729	chr5:75400467-75429015	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv526084	chr5:75410511-75530494	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75408200-75410600	Enhancers	Gastric	stomach
2	chr5:75409400-75411400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr5:75409400-75412200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:75409600-75410600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:75409600-75410600	Enhancers	Duodenum Mucosa	Duodenum
6	chr5:75409800-75410600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr5:75409800-75410600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:75409800-75410600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:75409800-75410600	Enhancers	Left Ventricle	heart
10	chr5:75409800-75410600	Enhancers	Lung	lung
11	chr5:75409800-75410600	Enhancers	HUVEC	blood vessel
12	chr5:75409800-75411000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr5:75409800-75411000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:75410000-75412800	Enhancers	Stomach Mucosa	stomach
15	chr5:75410200-75410600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:75410200-75410600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:75410200-75410600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr5:75410200-75411000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr5:75410200-75411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:75410400-75410600	Enhancers	Brain Anterior Caudate	brain
21	chr5:75410400-75410600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr5:75410400-75410600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
23	chr5:75410400-75410800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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