Variant report

Variant	rs6426169
Chromosome Location	chr1:224358912-224358913
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:224358899-224359153	U2OS	brain:	n/a	n/a
2	ZNF384	chr1:224358879-224359208	K562	blood:	n/a	n/a
3	MAX	chr1:224358828-224359145	K562	blood:	n/a	n/a
4	JUN	chr1:224358840-224359288	K562	blood:	n/a	n/a
5	BCLAF1	chr1:224358880-224359156	K562	blood:	n/a	n/a
6	NR2F2	chr1:224358866-224359216	K562	blood:	n/a	n/a
7	ZNF143	chr1:224358903-224359188	H1-hESC	embryonic stem cell:	n/a	n/a
8	PAX5	chr1:224358900-224359242	GM12892	blood:	n/a	n/a
9	JUND	chr1:224358866-224359267	K562	blood:	n/a	chr1:224359086-224359097
10	CBX3	chr1:224358845-224359251	K562	blood:	n/a	n/a
11	MAX	chr1:224358889-224359157	K562	blood:	n/a	n/a
12	ATF3	chr1:224358911-224359210	K562	blood:	n/a	n/a
13	SETDB1	chr1:224358901-224359191	U2OS	brain:	n/a	n/a
14	KAP1	chr1:224358252-224359245	K562	blood:	n/a	n/a
15	BATF	chr1:224358909-224359173	GM12878	blood:	n/a	n/a
16	JUND	chr1:224358745-224359235	SK-N-SH	brain:	n/a	chr1:224359086-224359097
17	JUND	chr1:224358908-224359248	HepG2	liver:	n/a	chr1:224359086-224359097
18	BCLAF1	chr1:224358784-224359169	K562	blood:	n/a	n/a
19	FOSL1	chr1:224358789-224359191	K562	blood:	n/a	n/a
20	TRIM28	chr1:224358852-224359162	K562	blood:	n/a	n/a
21	ZBTB7A	chr1:224358826-224359179	K562	blood:	n/a	n/a
22	CEBPB	chr1:224358883-224359204	K562	blood:	n/a	n/a
23	KAP1	chr1:224358846-224359187	HEK293	kidney:	n/a	n/a
24	TRIM28	chr1:224358733-224359326	K562	blood:	n/a	n/a
25	CBX3	chr1:224358705-224359299	K562	blood:	n/a	n/a
26	JUN	chr1:224358908-224359230	K562	blood:	n/a	n/a
27	FOSL1	chr1:224358862-224359230	K562	blood:	n/a	n/a
28	ZNF143	chr1:224358871-224359238	K562	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224358277..224359085-chr1:224520754..224521665,3	MCF-7	breast:

No data

Variant related genes	Relation type
DEGS1	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10753454	0.90[ASN][1000 genomes]
rs10799480	0.87[ASN][1000 genomes]
rs10799505	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916301	0.81[ASN][1000 genomes]
rs10916307	0.82[ASN][1000 genomes]
rs10916320	0.86[ASN][1000 genomes]
rs10916355	0.87[ASN][1000 genomes]
rs10916367	0.89[ASN][1000 genomes]
rs10916371	0.92[ASN][1000 genomes]
rs10916403	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916415	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11808787	0.82[ASN][1000 genomes]
rs12038372	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12049583	0.86[ASN][1000 genomes]
rs12070670	0.91[ASN][1000 genomes]
rs12076788	0.85[ASN][1000 genomes]
rs12563153	0.88[ASN][1000 genomes]
rs12730611	0.87[ASN][1000 genomes]
rs13374070	0.90[ASN][1000 genomes]
rs1492694	0.90[ASN][1000 genomes]
rs16844819	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17560970	0.87[ASN][1000 genomes]
rs1826421	0.92[ASN][1000 genomes]
rs2014782	0.88[ASN][1000 genomes]
rs2048997	0.81[ASN][1000 genomes]
rs2051105	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2172361	0.86[ASN][1000 genomes]
rs2280291	0.85[ASN][1000 genomes]
rs2404843	0.84[ASN][1000 genomes]
rs2896985	0.87[ASN][1000 genomes]
rs3767730	0.85[ASN][1000 genomes]
rs3820482	0.90[ASN][1000 genomes]
rs3820483	0.88[ASN][1000 genomes]
rs4653563	0.89[ASN][1000 genomes]
rs4653564	0.89[ASN][1000 genomes]
rs4653972	0.84[ASN][1000 genomes]
rs4653986	0.92[ASN][1000 genomes]
rs4653991	0.92[ASN][1000 genomes]
rs4653994	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653995	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55664906	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55736782	0.90[ASN][1000 genomes]
rs61827699	0.90[ASN][1000 genomes]
rs6426139	0.87[ASN][1000 genomes]
rs6426143	0.90[ASN][1000 genomes]
rs66506223	0.90[ASN][1000 genomes]
rs6657467	0.84[ASN][1000 genomes]
rs6658494	0.88[ASN][1000 genomes]
rs6659234	0.88[ASN][1000 genomes]
rs6680651	0.84[ASN][1000 genomes]
rs6682551	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685405	0.83[ASN][1000 genomes]
rs6685783	0.90[ASN][1000 genomes]
rs6688818	0.86[ASN][1000 genomes]
rs6690695	0.81[ASN][1000 genomes]
rs6691405	0.90[ASN][1000 genomes]
rs6698041	0.81[ASN][1000 genomes]
rs6700284	0.83[ASN][1000 genomes]
rs7511895	0.86[ASN][1000 genomes]
rs7518839	0.90[ASN][1000 genomes]
rs7524705	0.90[ASN][1000 genomes]
rs7526252	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7531891	0.90[ASN][1000 genomes]
rs7542293	0.90[ASN][1000 genomes]
rs7546235	0.90[ASN][1000 genomes]
rs8328	0.93[ASN][1000 genomes]
rs869945	0.88[ASN][1000 genomes]
rs908795	0.85[ASN][1000 genomes]
rs997296	0.92[ASN][1000 genomes]
rs997297	0.92[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6426169	FBXO28	cis	multi-tissue	Pritchard
rs6426169	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6426169	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224339200-224363200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:224345400-224363400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:224345600-224363400	Weak transcription	Ovary	ovary
5	chr1:224346400-224370000	Weak transcription	Esophagus	oesophagus
6	chr1:224346600-224363200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:224346600-224363200	Weak transcription	Fetal Stomach	stomach
8	chr1:224346600-224363400	Weak transcription	Right Ventricle	heart
9	chr1:224346600-224363400	Weak transcription	Spleen	Spleen
10	chr1:224355400-224359200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:224355600-224359000	Enhancers	Placenta	Placenta
12	chr1:224356000-224359000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:224356200-224359000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:224356200-224359000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr1:224356200-224359200	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:224356400-224359000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:224356400-224359000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:224356400-224359000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:224356400-224359000	Enhancers	NHEK	skin
20	chr1:224356800-224359000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:224357000-224359000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:224357000-224363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:224357200-224359000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:224357200-224359000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:224357200-224359200	Enhancers	Primary B cells from cord blood	blood
26	chr1:224357200-224359200	Enhancers	Primary T cells from cord blood	blood
27	chr1:224357200-224359200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:224357200-224363200	Weak transcription	Brain Substantia Nigra	brain
29	chr1:224357200-224363400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:224357800-224363200	Weak transcription	HUVEC	blood vessel
31	chr1:224358000-224363200	Weak transcription	Adipose Nuclei	Adipose
32	chr1:224358200-224359000	Enhancers	Small Intestine	intestine
33	chr1:224358200-224363400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:224358400-224359200	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr1:224358400-224363400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:224358600-224361200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:224358600-224362600	Weak transcription	Fetal Thymus	thymus
38	chr1:224358600-224363000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:224358600-224363000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:224358600-224363200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:224358600-224363200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:224358600-224363200	Weak transcription	HMEC	breast
43	chr1:224358600-224363400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:224358600-224363400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:224358800-224359000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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