Variant report

Variant	rs4653986
Chromosome Location	chr1:224330818-224330819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10753454	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799478	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799480	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916301	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916307	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916320	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916355	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916367	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916403	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916415	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11808787	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12038372	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12049583	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12070670	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12076788	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12563153	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12730611	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13374070	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492694	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16844819	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17560970	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1826421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011117	0.81[CHB][hapmap]
rs2014782	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2048997	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2051105	0.88[ASN][1000 genomes]
rs2172361	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280291	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2404843	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2896985	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767730	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3820482	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820483	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653563	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653568	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4653972	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653991	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653994	0.86[ASN][1000 genomes]
rs4653995	0.84[ASN][1000 genomes]
rs4654003	0.83[CHB][hapmap]
rs55664906	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55736782	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827699	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426139	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426143	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426169	0.92[ASN][1000 genomes]
rs6426178	0.86[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs66506223	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657467	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6658494	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6659234	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6680651	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6681673	0.83[CHB][hapmap]
rs6682292	0.83[CHB][hapmap]
rs6682551	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685405	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685783	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688818	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690695	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6691405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698041	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6700284	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7511895	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7518839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7531891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7542293	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7546235	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs869945	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs908795	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs908801	0.83[CHB][hapmap]
rs997296	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4653986	FBXO28	cis	multi-tissue	Pritchard
rs4653986	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs4653986	KIAA0483	cis	multi-tissue	Pritchard
rs4653986	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224314400-224333800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:224314400-224343400	Weak transcription	Psoas Muscle	Psoas
4	chr1:224315800-224331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:224316400-224331200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:224316600-224352200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:224317600-224333400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:224317800-224334000	Strong transcription	Fetal Intestine Large	intestine
9	chr1:224318000-224331200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:224318000-224332000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:224318200-224333400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:224318400-224331200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:224319200-224334000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:224319200-224335000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:224319800-224331200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:224320200-224344800	Weak transcription	Gastric	stomach
17	chr1:224320200-224345000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:224320200-224345000	Weak transcription	HUVEC	blood vessel
19	chr1:224320400-224344800	Weak transcription	Small Intestine	intestine
20	chr1:224320400-224345000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:224320400-224345000	Weak transcription	Right Ventricle	heart
22	chr1:224320400-224345200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:224320600-224344000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:224320600-224345000	Weak transcription	Pancreas	Pancrea
25	chr1:224320600-224345200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:224320800-224339000	Weak transcription	A549	lung
27	chr1:224320800-224343200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:224320800-224344200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:224320800-224344800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:224320800-224345200	Weak transcription	Brain Substantia Nigra	brain
31	chr1:224321000-224337200	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:224321000-224338400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:224321000-224343200	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:224321000-224343400	Weak transcription	Fetal Brain Male	brain
35	chr1:224321000-224344200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:224321000-224344800	Weak transcription	NHLF	lung
37	chr1:224321000-224345000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:224321000-224345400	Weak transcription	Fetal Heart	heart
39	chr1:224322000-224333400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:224322000-224345400	Weak transcription	HMEC	breast
41	chr1:224322400-224336200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:224322400-224337600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:224322600-224345000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:224322800-224331400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:224323000-224335400	Strong transcription	Fetal Intestine Small	intestine
46	chr1:224323000-224337000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:224323000-224337200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:224323000-224341000	Weak transcription	NH-A	brain
49	chr1:224323000-224343200	Weak transcription	NHDF-Ad	bronchial
50	chr1:224323200-224332200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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