Variant report

Variant	rs6426143
Chromosome Location	chr1:224318875-224318876
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	chr1:224316899..224321028-chr1:224322259..224326330,4	K562	blood:
2	chr1:224318706..224320701-chr1:224370372..224372701,2	K562	blood:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10753454	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799478	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799480	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799505	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916301	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916307	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916320	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916355	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916367	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916371	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916403	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916415	0.88[ASN][1000 genomes]
rs11808787	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12038372	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12049583	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12070670	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12076788	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12563153	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12730611	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13374070	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1492694	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844819	0.88[ASN][1000 genomes]
rs17560970	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1826421	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2014782	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2048997	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2051105	0.87[ASN][1000 genomes]
rs2172361	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280291	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2404843	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2896985	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767730	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820482	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820483	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653563	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653564	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653972	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653991	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653994	0.84[ASN][1000 genomes]
rs4653995	0.82[ASN][1000 genomes]
rs55664906	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55736782	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61827699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426139	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426169	0.90[ASN][1000 genomes]
rs66506223	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657467	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6658494	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6659234	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680651	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682551	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685405	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6685783	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688818	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690695	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6691405	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698041	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700284	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7511895	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7518839	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524705	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526252	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531891	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7542293	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7546235	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8328	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869945	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs908795	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs997296	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997297	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	nsv873222	chr1:224292898-224335422	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6426143	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6426143	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs6426143	FBXO28	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224302800-224319600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:224302800-224319600	Weak transcription	Esophagus	oesophagus
3	chr1:224302800-224319600	Weak transcription	Lung	lung
4	chr1:224302800-224319600	Weak transcription	Small Intestine	intestine
5	chr1:224302800-224320200	Weak transcription	Pancreas	Pancrea
6	chr1:224302800-224327200	Weak transcription	Aorta	Aorta
7	chr1:224303000-224329000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:224304000-224319600	Weak transcription	Fetal Stomach	stomach
10	chr1:224304400-224320000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:224310600-224319000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:224311800-224319600	Weak transcription	Gastric	stomach
13	chr1:224314400-224333800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:224314400-224343400	Weak transcription	Psoas Muscle	Psoas
15	chr1:224315600-224319600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:224315600-224319600	Weak transcription	Spleen	Spleen
17	chr1:224315800-224331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:224316400-224331200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:224316800-224319000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:224317200-224319800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:224317200-224329800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:224317600-224320800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:224317600-224321000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:224317600-224328400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:224317600-224333400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:224317800-224319400	ZNF genes & repeats	GM12878-XiMat	blood
28	chr1:224317800-224320000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:224317800-224320800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:224317800-224320800	Strong transcription	K562	blood
31	chr1:224317800-224321000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:224317800-224321000	Strong transcription	Ovary	ovary
33	chr1:224317800-224321000	Strong transcription	Thymus	Thymus
34	chr1:224317800-224321400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:224317800-224322600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:224317800-224323000	Strong transcription	Dnd41	blood
37	chr1:224317800-224325000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:224317800-224328200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:224317800-224328400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:224317800-224334000	Strong transcription	Fetal Intestine Large	intestine
41	chr1:224318000-224319000	ZNF genes & repeats	Brain Germinal Matrix	brain
42	chr1:224318000-224319200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:224318000-224319200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr1:224318000-224319400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:224318000-224320400	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:224318000-224320400	Strong transcription	Hela-S3	cervix
47	chr1:224318000-224320600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:224318000-224320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:224318000-224320800	Strong transcription	HSMMtube	muscle
50	chr1:224318000-224321000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links