Variant report

Variant	rs4653556
Chromosome Location	chr1:224254032-224254033
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224252218..224254539-chr1:224278231..224280105,2	K562	blood:
2	chr1:224253963..224257240-chr1:224261848..224265687,3	K562	blood:
3	chr1:224253604..224255684-chr1:224268887..224271520,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10753442	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753443	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10799460	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799463	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10799464	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916251	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916252	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916255	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916256	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10916257	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916259	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916264	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12028057	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12030540	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12062794	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12066952	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12120211	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12402838	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12402870	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403374	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388970	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492687	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492688	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492690	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492691	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492692	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1602711	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1602712	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1602713	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1873751	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1891742	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891743	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1935891	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2896918	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35805413	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653537	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653538	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653559	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653567	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653922	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653923	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653924	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653925	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653927	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4653928	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653992	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653993	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4654004	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4654005	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6426107	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6604884	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6604885	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6604886	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6604887	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661933	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6669606	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6678833	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6679769	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6680346	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6681233	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6681358	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6681461	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6683908	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6683927	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6684337	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6690580	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690667	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692043	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6693096	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695529	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6695935	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6696008	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696098	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6696212	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699110	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7524462	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7533263	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7535721	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7540585	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7540879	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7543043	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7543630	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7548255	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9662148	0.84[EUR][1000 genomes];0.83[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	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv160722	chr1:224253814-224254131	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653556	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs4653556	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224249600-224255200	Weak transcription	K562	blood
2	chr1:224249600-224256000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:224250600-224257800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:224252000-224254400	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr1:224252000-224256200	Enhancers	NHDF-Ad	bronchial
6	chr1:224252000-224256600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:224252400-224256200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:224252600-224254200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:224252600-224255000	Weak transcription	HSMM	muscle
10	chr1:224252600-224255400	Weak transcription	Small Intestine	intestine
11	chr1:224252600-224256200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:224252600-224258000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:224253200-224256000	Enhancers	HUVEC	blood vessel
14	chr1:224253400-224254400	Enhancers	NHLF	lung
15	chr1:224253400-224255000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:224253600-224255000	Weak transcription	NHEK	skin
17	chr1:224253600-224255000	Weak transcription	Osteobl	bone
18	chr1:224253600-224255400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:224253600-224255400	Weak transcription	NH-A	brain
20	chr1:224253800-224254200	Weak transcription	Stomach Mucosa	stomach
21	chr1:224253800-224254800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:224253800-224255000	Weak transcription	HMEC	breast
23	chr1:224253800-224255400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:224253800-224255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:224253800-224256000	Weak transcription	Fetal Intestine Large	intestine
26	chr1:224253800-224256000	Weak transcription	Fetal Intestine Small	intestine
27	chr1:224253800-224260400	Weak transcription	Pancreas	Pancrea
28	chr1:224254000-224254400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr1:224254000-224254800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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