Variant report

Variant	rs1258002
Chromosome Location	chr1:47094000-47094001
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	chr1:47093097..47096139-chr1:47100393..47103970,3	K562	blood:
2	chr1:47086033..47090385-chr1:47091411..47095597,5	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10158678	0.83[EUR][1000 genomes]
rs10159351	0.83[EUR][1000 genomes]
rs1025806	0.81[EUR][1000 genomes]
rs1048351	0.81[EUR][1000 genomes]
rs1075982	0.84[EUR][1000 genomes]
rs10890411	0.83[EUR][1000 genomes]
rs11211338	0.82[EUR][1000 genomes]
rs11211341	0.85[EUR][1000 genomes]
rs11211344	0.83[EUR][1000 genomes]
rs1139758	0.85[EUR][1000 genomes]
rs1150064	0.86[EUR][1000 genomes]
rs1150068	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11801316	0.83[EUR][1000 genomes]
rs11804665	0.85[EUR][1000 genomes]
rs12047537	0.84[EUR][1000 genomes]
rs12078635	0.83[EUR][1000 genomes]
rs12094663	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1258000	0.94[EUR][1000 genomes]
rs1258001	0.84[EUR][1000 genomes]
rs1258003	0.88[EUR][1000 genomes]
rs1258004	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1258052	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258053	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258054	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258056	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258059	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13417	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1440486	0.81[EUR][1000 genomes]
rs1440489	0.82[EUR][1000 genomes]
rs17102352	0.85[EUR][1000 genomes]
rs17102355	0.85[EUR][1000 genomes]
rs1745377	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1933933	0.84[EUR][1000 genomes]
rs1962900	0.81[EUR][1000 genomes]
rs2083486	0.83[EUR][1000 genomes]
rs2119301	0.81[EUR][1000 genomes]
rs2218189	0.83[EUR][1000 genomes]
rs2241862	0.86[EUR][1000 genomes]
rs2289446	0.84[EUR][1000 genomes]
rs2289447	0.81[EUR][1000 genomes]
rs2304745	0.81[EUR][1000 genomes]
rs2405026	0.81[EUR][1000 genomes]
rs2405030	0.83[EUR][1000 genomes]
rs34932727	0.81[EUR][1000 genomes]
rs3737731	0.81[EUR][1000 genomes]
rs3766211	0.82[EUR][1000 genomes]
rs3766212	0.82[EUR][1000 genomes]
rs3766214	0.83[EUR][1000 genomes]
rs3766215	0.81[EUR][1000 genomes]
rs3766217	0.81[EUR][1000 genomes]
rs3766219	0.86[EUR][1000 genomes]
rs3766224	0.86[EUR][1000 genomes]
rs4272563	0.83[EUR][1000 genomes]
rs4274009	0.80[EUR][1000 genomes]
rs4301586	0.83[EUR][1000 genomes]
rs4443838	0.84[EUR][1000 genomes]
rs58185502	0.81[EUR][1000 genomes]
rs585257	0.81[EUR][1000 genomes]
rs594118	0.87[EUR][1000 genomes]
rs595813	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59881815	0.84[EUR][1000 genomes]
rs60173509	0.84[EUR][1000 genomes]
rs60675294	0.81[EUR][1000 genomes]
rs611468	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs614486	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61782563	0.81[EUR][1000 genomes]
rs61782564	0.81[EUR][1000 genomes]
rs61782568	0.81[EUR][1000 genomes]
rs61784001	0.84[EUR][1000 genomes]
rs61784002	0.84[EUR][1000 genomes]
rs61784003	0.82[EUR][1000 genomes]
rs618554	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs620431	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs620913	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs625507	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs625590	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs637760	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs638845	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6429607	0.81[EUR][1000 genomes]
rs647999	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6656244	0.82[EUR][1000 genomes]
rs6666405	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6667885	0.81[EUR][1000 genomes]
rs6669393	0.85[EUR][1000 genomes]
rs6671005	0.81[EUR][1000 genomes]
rs6671124	0.84[EUR][1000 genomes]
rs6688195	0.81[EUR][1000 genomes]
rs723334	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs732539	0.82[EUR][1000 genomes]
rs7354865	0.83[EUR][1000 genomes]
rs7412469	0.81[EUR][1000 genomes]
rs744096	0.84[EUR][1000 genomes]
rs7532601	0.83[EUR][1000 genomes]
rs7541868	0.82[EUR][1000 genomes]
rs946320	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv522319	chr1:47080741-47094267	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
5	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1258002	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47083000-47094400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:47083000-47094600	Weak transcription	Right Ventricle	heart
3	chr1:47083000-47097200	Weak transcription	Gastric	stomach
4	chr1:47083000-47100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:47083200-47094400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:47083200-47094600	Weak transcription	Liver	Liver
7	chr1:47083200-47095400	Weak transcription	Fetal Thymus	thymus
8	chr1:47083200-47095600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:47083200-47097200	Weak transcription	Primary B cells from cord blood	blood
10	chr1:47083200-47097200	Weak transcription	Aorta	Aorta
11	chr1:47083200-47097200	Weak transcription	Thymus	Thymus
12	chr1:47083200-47100200	Weak transcription	Psoas Muscle	Psoas
13	chr1:47083200-47104600	Weak transcription	Stomach Mucosa	stomach
14	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:47083400-47094200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:47083400-47094200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:47083400-47094600	Weak transcription	Adipose Nuclei	Adipose
18	chr1:47083400-47094800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:47083400-47095000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:47083400-47095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:47083400-47095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:47083400-47095600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:47083400-47095600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:47083400-47096800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:47083400-47097000	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:47083400-47097400	Weak transcription	Brain Substantia Nigra	brain
27	chr1:47083400-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:47083600-47094200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:47084800-47094600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:47084800-47097000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:47085600-47099000	Weak transcription	GM12878-XiMat	blood
32	chr1:47085800-47097200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:47085800-47097600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:47087800-47097000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:47088000-47098000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:47088000-47100800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:47088200-47095000	Weak transcription	HSMM	muscle
38	chr1:47088200-47097000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:47088200-47097200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:47088200-47097200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:47088200-47097200	Weak transcription	NH-A	brain
42	chr1:47088200-47097400	Weak transcription	Osteobl	bone
43	chr1:47088200-47097800	Weak transcription	HSMMtube	muscle
44	chr1:47088200-47097800	Weak transcription	NHDF-Ad	bronchial
45	chr1:47088200-47098000	Weak transcription	Colonic Mucosa	Colon
46	chr1:47088200-47100000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:47088200-47100000	Weak transcription	Spleen	Spleen
48	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr1:47088400-47094600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:47088400-47095600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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