Variant report

Variant	rs6682292
Chromosome Location	chr1:224400175-224400176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr1:224400048-224400835	HEK293-T-REx	kidney:	n/a	n/a
2	GATA3	chr1:224400038-224400913	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr1:224400126-224400797	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000232628	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10799505	0.81[CHB][hapmap]
rs10916301	0.81[CHB][hapmap]
rs10916371	0.82[CHB][hapmap]
rs10916415	0.82[CHB][hapmap]
rs12038372	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12049583	0.82[CHB][hapmap]
rs16844819	0.81[CHB][hapmap]
rs17560970	0.83[CHB][hapmap]
rs1826421	0.81[CHB][hapmap]
rs2011117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172361	0.83[CHB][hapmap]
rs2176600	0.82[CEU][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs2404843	0.81[CHB][hapmap]
rs2896985	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs3767730	0.81[CHB][hapmap]
rs3820482	0.83[CHB][hapmap]
rs3820483	0.86[CHB][hapmap]
rs4653564	0.86[CHB][hapmap]
rs4653568	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]
rs4653569	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653986	0.83[CHB][hapmap]
rs4654000	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4654003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426139	0.83[CHB][hapmap]
rs6426178	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs6658494	0.83[CHB][hapmap]
rs6659234	0.83[CHB][hapmap]
rs6669401	0.83[AMR][1000 genomes]
rs6678942	0.82[AMR][1000 genomes]
rs6681673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685783	0.83[CHB][hapmap]
rs6691405	0.83[CHB][hapmap]
rs6700284	0.83[CHB][hapmap]
rs7511895	0.81[CHB][hapmap]
rs7518839	0.81[CHB][hapmap]
rs7524705	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7526252	0.81[CHB][hapmap]
rs7531891	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs8328	0.81[CHB][hapmap]
rs869945	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs908801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9793489	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997297	0.83[CHB][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6682292	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6682292	FBXO28	cis	multi-tissue	Pritchard
rs6682292	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 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	chr1:224391600-224400200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:224392600-224400400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:224393600-224400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:224393600-224400200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:224393600-224400200	Weak transcription	Gastric	stomach
8	chr1:224393600-224400400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:224393600-224400400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:224393600-224400800	Weak transcription	Right Atrium	heart
11	chr1:224393600-224401200	Weak transcription	Esophagus	oesophagus
12	chr1:224393600-224401200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:224393800-224400200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:224393800-224400200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:224393800-224400200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:224393800-224400200	Weak transcription	HSMMtube	muscle
17	chr1:224393800-224405600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
19	chr1:224394000-224400800	Weak transcription	HSMM	muscle
20	chr1:224394000-224401200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:224394000-224414600	Weak transcription	HMEC	breast
23	chr1:224394400-224400400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:224394400-224400600	Weak transcription	K562	blood
25	chr1:224394400-224400800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:224394600-224400200	Weak transcription	Small Intestine	intestine
27	chr1:224396800-224402200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:224397000-224401800	Enhancers	Fetal Muscle Leg	muscle
29	chr1:224397600-224402200	Enhancers	Fetal Intestine Small	intestine
30	chr1:224397600-224402400	Enhancers	Stomach Mucosa	stomach
31	chr1:224397800-224400400	Enhancers	Duodenum Mucosa	Duodenum
32	chr1:224397800-224402400	Enhancers	HepG2	liver
33	chr1:224398000-224401600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:224398000-224402400	Enhancers	Fetal Intestine Large	intestine
35	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
36	chr1:224398200-224400200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:224398200-224400200	Weak transcription	Right Ventricle	heart
38	chr1:224398200-224401200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:224398200-224401200	Weak transcription	GM12878-XiMat	blood
40	chr1:224398400-224401400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:224398600-224400200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:224398600-224400200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:224398600-224401800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr1:224398800-224400200	Enhancers	NHEK	skin
45	chr1:224398800-224401000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr1:224398800-224401400	Enhancers	Hela-S3	cervix
47	chr1:224398800-224401800	Enhancers	Placenta Amnion	Placenta Amnion
48	chr1:224399000-224400400	Enhancers	NH-A	brain
49	chr1:224399000-224400400	Enhancers	NHLF	lung
50	chr1:224399000-224402200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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