Variant report

Variant	rs12730611
Chromosome Location	chr1:224319825-224319826
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224319528..224321607-chr1:224321881..224324191,2	K562	blood:
2	chr1:224313532..224316324-chr1:224319519..224321918,2	K562	blood:
3	chr1:224316899..224321028-chr1:224322259..224326330,4	K562	blood:
4	chr1:224318706..224320701-chr1:224370372..224372701,2	K562	blood:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10753454	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10799478	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10799480	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799505	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916301	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916307	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916320	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916355	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916367	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916371	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916403	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916415	0.85[ASN][1000 genomes]
rs11808787	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12038372	0.83[ASN][1000 genomes]
rs12049583	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12070670	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12076788	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12563153	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13374070	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1492694	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16844819	0.85[ASN][1000 genomes]
rs17560970	0.94[ASN][1000 genomes]
rs1826421	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014782	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2048997	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2051105	0.84[ASN][1000 genomes]
rs2172361	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280291	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2404843	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2896985	0.94[ASN][1000 genomes]
rs3767730	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820482	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3820483	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653563	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653564	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653972	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653986	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653991	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653994	0.81[ASN][1000 genomes]
rs55664906	0.85[ASN][1000 genomes]
rs55736782	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827699	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426139	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426143	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426169	0.87[ASN][1000 genomes]
rs66506223	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6657467	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6658494	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6659234	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680651	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682551	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685405	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6685783	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688818	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6690695	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6691405	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698041	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6700284	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7511895	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518839	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524705	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7526252	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7531891	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7542293	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546235	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8328	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs869945	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs908795	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs997296	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997297	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12730611	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs12730611	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224302800-224320200	Weak transcription	Pancreas	Pancrea
2	chr1:224302800-224327200	Weak transcription	Aorta	Aorta
3	chr1:224303000-224329000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:224304400-224320000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:224314400-224333800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:224314400-224343400	Weak transcription	Psoas Muscle	Psoas
8	chr1:224315800-224331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:224316400-224331200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:224317200-224329800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:224317600-224320800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:224317600-224321000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:224317600-224328400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:224317600-224333400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:224317800-224320000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:224317800-224320800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:224317800-224320800	Strong transcription	K562	blood
19	chr1:224317800-224321000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:224317800-224321000	Strong transcription	Ovary	ovary
21	chr1:224317800-224321000	Strong transcription	Thymus	Thymus
22	chr1:224317800-224321400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:224317800-224322600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr1:224317800-224323000	Strong transcription	Dnd41	blood
25	chr1:224317800-224325000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:224317800-224328200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:224317800-224328400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:224317800-224334000	Strong transcription	Fetal Intestine Large	intestine
29	chr1:224318000-224320400	Strong transcription	Fetal Muscle Leg	muscle
30	chr1:224318000-224320400	Strong transcription	Hela-S3	cervix
31	chr1:224318000-224320600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:224318000-224320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:224318000-224320800	Strong transcription	HSMMtube	muscle
34	chr1:224318000-224321000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:224318000-224321000	Strong transcription	Brain Angular Gyrus	brain
36	chr1:224318000-224321000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:224318000-224321000	Strong transcription	Fetal Brain Male	brain
38	chr1:224318000-224321200	Strong transcription	Primary T cells from cord blood	blood
39	chr1:224318000-224323000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:224318000-224323400	Strong transcription	Liver	Liver
41	chr1:224318000-224324200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:224318000-224324200	Strong transcription	HepG2	liver
43	chr1:224318000-224324400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:224318000-224328400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr1:224318000-224328400	Strong transcription	Fetal Thymus	thymus
46	chr1:224318000-224328600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:224318000-224329600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr1:224318000-224330600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:224318000-224331200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:224318000-224332000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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