Variant report

Variant	rs4653568
Chromosome Location	chr1:224396329-224396330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224394938..224397843-chr1:224400035..224402726,3	K562	blood:
2	chr1:224394938..224396806-chr1:224401226..224402970,2	K562	blood:

Variant related genes	Relation type
ENSG00000232628	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10799505	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10916301	0.81[CHB][hapmap]
rs10916371	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs10916415	0.80[CHB][hapmap]
rs12038372	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs12049583	0.81[CHB][hapmap]
rs16844819	0.81[CHB][hapmap]
rs17560970	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1826421	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2011117	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172361	0.81[CHB][hapmap]
rs2176600	0.82[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs2404843	0.81[CHB][hapmap]
rs2896985	0.81[CHB][hapmap]
rs3767730	0.81[CHB][hapmap]
rs3820482	0.81[CHB][hapmap]
rs3820483	0.85[CHB][hapmap]
rs4653564	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4653569	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653986	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4654000	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4654003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426139	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6426178	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs6658494	0.81[CHB][hapmap]
rs6659234	0.81[CHB][hapmap]
rs6669401	0.81[AMR][1000 genomes]
rs6678942	0.81[AMR][1000 genomes]
rs6681673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685783	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6688818	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6691405	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6700284	0.81[CHB][hapmap]
rs7511895	0.81[CHB][hapmap]
rs7518839	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7524705	0.81[CHB][hapmap]
rs7526252	0.81[CHB][hapmap]
rs7531891	0.81[CHB][hapmap]
rs8328	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs869945	0.81[CHB][hapmap]
rs908801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9793489	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs997297	0.81[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4653568	BPNT1	cis	parietal	SCAN
rs4653568	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs4653568	DEGS1	cis	multi-tissue	Pritchard
rs4653568	SUSD4	cis	parietal	SCAN
rs4653568	FBXO28	cis	lymphoblastoid	seeQTL
rs4653568	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4653568	FBXO28	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224391600-224400000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:224391600-224400200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:224392600-224400400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:224393400-224399000	Weak transcription	Brain Germinal Matrix	brain
7	chr1:224393600-224397000	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:224393600-224397200	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:224393600-224397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:224393600-224397600	Weak transcription	Left Ventricle	heart
11	chr1:224393600-224397600	Weak transcription	Spleen	Spleen
12	chr1:224393600-224397800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:224393600-224397800	Weak transcription	Right Ventricle	heart
14	chr1:224393600-224398800	Weak transcription	Brain Substantia Nigra	brain
15	chr1:224393600-224398800	Weak transcription	Fetal Kidney	kidney
16	chr1:224393600-224399000	Weak transcription	Brain Anterior Caudate	brain
17	chr1:224393600-224399000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:224393600-224399000	Weak transcription	Psoas Muscle	Psoas
19	chr1:224393600-224399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:224393600-224399200	Weak transcription	Lung	lung
21	chr1:224393600-224400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:224393600-224400200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:224393600-224400200	Weak transcription	Gastric	stomach
24	chr1:224393600-224400400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:224393600-224400400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:224393600-224400800	Weak transcription	Right Atrium	heart
27	chr1:224393600-224401200	Weak transcription	Esophagus	oesophagus
28	chr1:224393600-224401200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:224393800-224397200	Weak transcription	GM12878-XiMat	blood
30	chr1:224393800-224397800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:224393800-224398000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:224393800-224398000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:224393800-224398600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:224393800-224398800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:224393800-224398800	Weak transcription	Fetal Heart	heart
36	chr1:224393800-224398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:224393800-224398800	Weak transcription	Fetal Lung	lung
38	chr1:224393800-224398800	Weak transcription	Fetal Stomach	stomach
39	chr1:224393800-224399000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:224393800-224399000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:224393800-224399000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:224393800-224399000	Weak transcription	NH-A	brain
43	chr1:224393800-224399200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:224393800-224400200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:224393800-224400200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:224393800-224400200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:224393800-224400200	Weak transcription	HSMMtube	muscle
48	chr1:224393800-224405600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
50	chr1:224394000-224398800	Weak transcription	Placenta Amnion	Placenta Amnion

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