Variant report

Variant	rs727484
Chromosome Location	chr16:58790472-58790473
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:58546668..58549443-chr16:58789792..58791379,2	K562	blood:
2	chr16:58712427..58713373-chr16:58789987..58790958,13	MCF-7	breast:
3	chr16:58767841..58768621-chr16:58790451..58790986,2	MCF-7	breast:
4	chr16:58545471..58546477-chr16:58789997..58790949,4	K562	blood:

Variant related genes	Relation type
ENSG00000103042	Chromatin interaction
ENSG00000103037	Chromatin interaction
ENSG00000125166	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs11076259	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11076260	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11076262	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11649636	0.85[AMR][1000 genomes]
rs11649637	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12325516	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12709012	0.99[EUR][1000 genomes]
rs12924243	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1369933	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1369934	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1436427	0.87[EUR][1000 genomes]
rs149479	0.83[EUR][1000 genomes]
rs1595180	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1595181	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1616072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616798	0.87[JPT][hapmap]
rs1618602	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1624301	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626006	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646256	0.81[EUR][1000 genomes]
rs1646260	0.88[EUR][1000 genomes]
rs1646265	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646268	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1646269	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1646274	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1646275	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1646278	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646279	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646280	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646281	0.99[EUR][1000 genomes]
rs1646282	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1646284	0.99[EUR][1000 genomes]
rs1646285	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1646286	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646287	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1646288	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657161	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1657163	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657164	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657166	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1657167	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1657169	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657171	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657176	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657177	0.91[EUR][1000 genomes]
rs1657178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1657179	0.87[JPT][hapmap]
rs166290	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1865836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs191783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2406087	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2432621	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2432622	0.95[EUR][1000 genomes]
rs2575374	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs257627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs257628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs257629	0.99[EUR][1000 genomes]
rs30834	0.84[EUR][1000 genomes]
rs30836	0.80[EUR][1000 genomes]
rs30837	0.84[EUR][1000 genomes]
rs30838	0.85[EUR][1000 genomes]
rs30840	0.83[EUR][1000 genomes]
rs30841	0.83[EUR][1000 genomes]
rs30842	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4238801	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4315316	0.99[EUR][1000 genomes]
rs4427787	0.85[EUR][1000 genomes]
rs4499224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4538000	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4575523	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4784977	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4784982	0.82[EUR][1000 genomes]
rs6499974	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6499976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6499984	0.87[EUR][1000 genomes]
rs6499985	0.81[EUR][1000 genomes]
rs6993	0.88[CEU][hapmap]
rs7184377	0.88[EUR][1000 genomes]
rs7188608	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7194961	0.81[EUR][1000 genomes]
rs72792430	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044542	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8045466	0.99[EUR][1000 genomes]
rs8046154	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs8049462	0.99[EUR][1000 genomes]
rs8051078	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8054414	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8060717	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8060721	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs839418	0.83[EUR][1000 genomes]
rs899375	0.88[EUR][1000 genomes]
rs9302706	0.87[EUR][1000 genomes]
rs9937713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
4	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs727484	GOT2	cis	Skin Sun Exposed Lower leg	GTEx
rs727484	GOT2	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58789600-58790600	Enhancers	Primary hematopoietic stem cells	blood
2	chr16:58789600-58790600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr16:58789600-58791000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr16:58789800-58790600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr16:58789800-58790600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:58789800-58790600	Flanking Active TSS	Dnd41	blood
7	chr16:58789800-58790600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr16:58790000-58790600	Active TSS	Brain Hippocampus Middle	brain
9	chr16:58790000-58790600	Enhancers	Spleen	Spleen
10	chr16:58790000-58791200	Enhancers	Liver	Liver
11	chr16:58790200-58790600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr16:58790400-58790600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr16:58790400-58790600	Enhancers	Primary B cells from peripheral blood	blood
14	chr16:58790400-58790600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr16:58790400-58790600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr16:58790400-58790600	Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr16:58790400-58790600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr16:58790400-58790600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr16:58790400-58790600	Enhancers	Brain Anterior Caudate	brain
20	chr16:58790400-58791400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr16:58790400-58800200	Weak transcription	Fetal Brain Male	brain

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