Variant report

Variant	rs16889865
Chromosome Location	chr5:58755220-58755221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1120303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1156028	0.87[ASN][1000 genomes]
rs1457110	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16889853	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16889869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16889892	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs174039	0.83[ASN][1000 genomes]
rs17796040	0.81[TSI][hapmap]
rs1824154	0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1902610	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2081092	0.88[GIH][hapmap];0.82[JPT][hapmap];0.85[MKK][hapmap]
rs28666954	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28729916	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35450986	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3852147	0.87[ASN][1000 genomes]
rs41447947	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56173502	0.88[EUR][1000 genomes]
rs56349317	0.95[EUR][1000 genomes]
rs58232524	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59152084	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59246284	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60509830	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6870632	0.89[LWK][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6871710	0.83[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs73097356	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7704141	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7711639	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs7737908	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs988827	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs988828	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1034656	chr5:58674724-58755580	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv881707	chr5:58741491-58784102	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv275451	chr5:58754377-58755220	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16889865	C5orf35	cis	cerebellum	SCAN
rs16889865	PART1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58709800-58756800	Weak transcription	Aorta	Aorta
2	chr5:58716000-58756600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:58731800-58764800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:58735800-58756400	Weak transcription	Psoas Muscle	Psoas
5	chr5:58750400-58756200	Weak transcription	Fetal Stomach	stomach
6	chr5:58751600-58755400	Weak transcription	Fetal Kidney	kidney
7	chr5:58752200-58756600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:58752400-58756400	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:58753600-58767400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:58753800-58755400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr5:58753800-58755800	Enhancers	Fetal Intestine Large	intestine
12	chr5:58753800-58757600	Enhancers	Fetal Intestine Small	intestine
13	chr5:58754600-58756200	Weak transcription	Fetal Brain Male	brain
14	chr5:58754600-58759200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:58754600-58760800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:58754600-58780200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:58754800-58755400	Weak transcription	Fetal Brain Female	brain
18	chr5:58755000-58755600	Flanking Active TSS	Liver	Liver
19	chr5:58755000-58759200	Genic enhancers	A549	lung
20	chr5:58755200-58755400	Enhancers	Pancreas	Pancrea

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