Variant report

Variant	rs12514658
Chromosome Location	chr5:58774961-58774962
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10514863	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1156029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12521370	0.95[EUR][1000 genomes]
rs1457112	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1506557	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16889876	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16889882	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16889883	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16889885	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16889896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1848059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034893	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2034894	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2161513	0.95[EUR][1000 genomes]
rs28424104	0.90[ASN][1000 genomes]
rs28508065	0.90[ASN][1000 genomes]
rs28571683	0.85[ASN][1000 genomes]
rs28706428	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72767785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724786	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931855	0.83[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs992726	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9942415	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58754600-58780200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:58756800-58775400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr5:58756800-58775600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:58762000-58778800	Weak transcription	Aorta	Aorta
5	chr5:58762600-58780600	Weak transcription	Fetal Lung	lung
6	chr5:58768800-58779400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:58770200-58779400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:58772200-58776200	Weak transcription	Psoas Muscle	Psoas
9	chr5:58773800-58776400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:58774000-58783600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:58774600-58783000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:58774800-58775000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr5:58774800-58775200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr5:58774800-58775200	Enhancers	Brain Substantia Nigra	brain
15	chr5:58774800-58775400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr5:58774800-58775400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:58774800-58775400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr5:58774800-58775600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:58774800-58775800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:58774800-58779000	Genic enhancers	A549	lung

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