Variant report

Variant	rs244579
Chromosome Location	chr5:58665935-58665936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs154031	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs165940	0.83[EUR][1000 genomes]
rs168641	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16889733	0.83[EUR][1000 genomes]
rs187368	0.83[EUR][1000 genomes]
rs2441091	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs244573	0.87[AFR][1000 genomes]
rs244574	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs244577	0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs244580	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs244581	0.92[ASN][1000 genomes]
rs244582	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs244583	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs244586	0.82[ASN][1000 genomes]
rs244587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs244588	0.95[CHB][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs244590	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs244591	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs244592	0.83[EUR][1000 genomes]
rs244593	0.83[EUR][1000 genomes]
rs244594	0.82[EUR][1000 genomes]
rs244595	0.83[EUR][1000 genomes]
rs244596	0.83[EUR][1000 genomes]
rs244597	0.83[EUR][1000 genomes]
rs258128	0.82[CEU][hapmap]
rs35258	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs35267	0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs35274	1.00[YRI][hapmap]
rs35276	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs35277	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs35278	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs35279	0.87[AFR][1000 genomes]
rs35283	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs35284	0.89[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs365223	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs368538	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs370891	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs378858	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs380993	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs383046	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs387647	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs39672	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs40126	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs40328	1.00[YRI][hapmap]
rs403672	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs403695	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs424839	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs427433	0.83[EUR][1000 genomes]
rs428059	0.83[EUR][1000 genomes]
rs431645	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs432879	0.81[EUR][1000 genomes]
rs433161	0.83[EUR][1000 genomes]
rs434183	0.81[EUR][1000 genomes]
rs434274	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs434422	0.83[EUR][1000 genomes]
rs441817	0.83[EUR][1000 genomes]
rs444552	0.83[EUR][1000 genomes]
rs454702	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs530656	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs531511	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1032732	chr5:58637179-58689010	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1022160	chr5:58645805-58689010	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv881704	chr5:58653383-58675538	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58653000-58669400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:58654400-58667000	Weak transcription	Fetal Intestine Large	intestine
3	chr5:58659800-58667200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:58660600-58669200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:58663800-58666400	Enhancers	A549	lung
6	chr5:58665400-58666000	Enhancers	Psoas Muscle	Psoas
7	chr5:58665600-58666000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:58665800-58666000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:58665800-58666000	Enhancers	Rectal Smooth Muscle	rectum

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