Variant report

Variant	rs58891772
Chromosome Location	chr3:112264872-112264873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112263776..112266083-chr3:112359451..112361414,2	MCF-7	breast:
2	chr3:112259312..112262688-chr3:112264103..112268109,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10511317	0.92[EUR][1000 genomes]
rs11919639	0.89[EUR][1000 genomes]
rs11921669	0.89[EUR][1000 genomes]
rs13059364	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13063173	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13064534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065703	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070342	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080547	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13080749	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13081201	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13081265	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13081632	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13088339	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13088349	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13088467	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13092057	0.85[EUR][1000 genomes]
rs13094161	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13094649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095000	0.92[EUR][1000 genomes]
rs13096943	0.96[EUR][1000 genomes]
rs16845067	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16859661	0.96[EUR][1000 genomes]
rs16859674	0.89[EUR][1000 genomes]
rs16859727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859758	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16859779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16859787	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859793	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2220656	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2705526	0.92[EUR][1000 genomes]
rs28365853	0.92[EUR][1000 genomes]
rs34080815	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139211	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34248586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34284082	0.89[EUR][1000 genomes]
rs34541731	0.92[EUR][1000 genomes]
rs34596334	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34597203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645913	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34829517	0.92[EUR][1000 genomes]
rs34889961	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34949685	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34962178	0.92[EUR][1000 genomes]
rs35107041	0.89[EUR][1000 genomes]
rs35240469	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255669	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35349986	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35512450	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526995	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35529363	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35692417	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35709173	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35725070	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35748518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35803911	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35840933	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35931975	0.92[EUR][1000 genomes]
rs36025914	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36031379	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36045008	0.92[EUR][1000 genomes]
rs36061184	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36146261	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs36153507	0.92[EUR][1000 genomes]
rs3736269	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773698	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773701	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773704	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773706	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773710	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3821684	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55742760	0.92[EUR][1000 genomes]
rs56662636	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56856838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56970524	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs57346109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59279185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59305071	0.94[AFR][1000 genomes]
rs59858117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60321074	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60646325	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66486470	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66698345	0.89[EUR][1000 genomes]
rs66791711	0.92[EUR][1000 genomes]
rs66910014	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67021100	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67204151	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67513863	0.89[EUR][1000 genomes]
rs67940544	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs67944354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317505	0.92[EUR][1000 genomes]
rs71317506	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71317507	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317508	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71317510	0.92[EUR][1000 genomes]
rs724125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229350	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229353	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73229398	0.92[EUR][1000 genomes]
rs958935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58891772	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
6	chr3:112244400-112278200	Weak transcription	K562	blood
7	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
8	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:112247000-112267800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:112247600-112279600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:112247800-112265800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:112248400-112265600	Weak transcription	Brain Germinal Matrix	brain
14	chr3:112248400-112266200	Weak transcription	Brain Anterior Caudate	brain
15	chr3:112248400-112274200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:112248800-112265000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:112249000-112265400	Weak transcription	Right Ventricle	heart
18	chr3:112249200-112265000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:112249200-112265800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:112249200-112269800	Weak transcription	Psoas Muscle	Psoas
21	chr3:112249200-112275800	Weak transcription	Fetal Stomach	stomach
22	chr3:112249200-112276000	Weak transcription	Spleen	Spleen
23	chr3:112249200-112278200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:112249200-112278400	Weak transcription	Aorta	Aorta
25	chr3:112249200-112279600	Weak transcription	Esophagus	oesophagus
26	chr3:112249200-112279600	Weak transcription	Gastric	stomach
27	chr3:112249200-112279800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:112249400-112270000	Weak transcription	Fetal Intestine Small	intestine
29	chr3:112249400-112276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:112249400-112279600	Weak transcription	Lung	lung
31	chr3:112249600-112265000	Weak transcription	Colonic Mucosa	Colon
32	chr3:112251000-112274200	Weak transcription	Brain Angular Gyrus	brain
33	chr3:112251200-112268200	Strong transcription	Liver	Liver
34	chr3:112252200-112270200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:112252400-112269800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:112252600-112278400	Weak transcription	Fetal Kidney	kidney
37	chr3:112252800-112265200	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:112253000-112273400	Weak transcription	Brain Substantia Nigra	brain
39	chr3:112253200-112278600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:112254200-112273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:112254800-112265000	Weak transcription	A549	lung
42	chr3:112255000-112265000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:112257600-112274000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:112258000-112265000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:112258000-112266200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:112258000-112267400	Weak transcription	NH-A	brain
47	chr3:112258800-112268000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:112259200-112270400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:112259400-112265800	Weak transcription	Hela-S3	cervix
50	chr3:112259600-112268600	Strong transcription	Placenta	Placenta

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