Variant report

Variant	rs61782568
Chromosome Location	chr1:47171101-47171102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47166087..47167615-chr1:47169946..47172468,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10158678	0.98[EUR][1000 genomes]
rs10159351	0.98[EUR][1000 genomes]
rs1025806	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048351	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1048380	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1075982	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10890411	0.98[EUR][1000 genomes]
rs11211338	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211341	0.93[EUR][1000 genomes]
rs11211344	0.98[EUR][1000 genomes]
rs11211346	0.94[EUR][1000 genomes]
rs1139758	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1150064	0.94[EUR][1000 genomes]
rs1150068	0.91[EUR][1000 genomes]
rs11801316	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11801419	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11804665	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12047537	0.96[EUR][1000 genomes]
rs12078635	0.98[EUR][1000 genomes]
rs12082387	0.91[EUR][1000 genomes]
rs12094663	0.93[EUR][1000 genomes]
rs1258000	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1258002	0.81[EUR][1000 genomes]
rs1258003	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1258052	0.91[EUR][1000 genomes]
rs1258053	0.90[EUR][1000 genomes]
rs1258054	0.91[EUR][1000 genomes]
rs1258056	0.91[EUR][1000 genomes]
rs1258059	0.91[EUR][1000 genomes]
rs13417	0.94[EUR][1000 genomes]
rs1440486	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440489	0.86[EUR][1000 genomes]
rs17102352	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17102355	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17102473	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1745377	0.91[EUR][1000 genomes]
rs1933933	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1962900	0.95[EUR][1000 genomes]
rs2083486	0.98[EUR][1000 genomes]
rs2119301	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2218189	0.98[EUR][1000 genomes]
rs2241862	0.94[EUR][1000 genomes]
rs2289446	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2289447	0.94[EUR][1000 genomes]
rs2304745	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405030	0.97[EUR][1000 genomes]
rs34932727	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737731	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766211	0.96[EUR][1000 genomes]
rs3766212	0.96[EUR][1000 genomes]
rs3766214	0.98[EUR][1000 genomes]
rs3766215	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766217	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766219	0.94[EUR][1000 genomes]
rs3766224	0.94[EUR][1000 genomes]
rs4272563	0.97[EUR][1000 genomes]
rs4274009	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4301586	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4443838	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55914029	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56319728	0.82[EUR][1000 genomes]
rs58185502	0.94[EUR][1000 genomes]
rs585257	0.93[EUR][1000 genomes]
rs594118	0.93[EUR][1000 genomes]
rs595813	0.93[EUR][1000 genomes]
rs59881815	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60173509	0.96[EUR][1000 genomes]
rs60675294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611468	0.93[EUR][1000 genomes]
rs614486	0.94[EUR][1000 genomes]
rs61782563	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61782564	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61782590	0.86[EUR][1000 genomes]
rs61784001	0.96[EUR][1000 genomes]
rs61784002	0.96[EUR][1000 genomes]
rs61784003	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618554	0.91[EUR][1000 genomes]
rs620431	0.91[EUR][1000 genomes]
rs620913	0.91[EUR][1000 genomes]
rs625507	0.93[EUR][1000 genomes]
rs625590	0.94[EUR][1000 genomes]
rs637760	0.93[EUR][1000 genomes]
rs638845	0.94[EUR][1000 genomes]
rs6429607	0.94[EUR][1000 genomes]
rs6429608	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6429609	0.86[EUR][1000 genomes]
rs647999	0.88[EUR][1000 genomes]
rs6656244	0.86[ASN][1000 genomes]
rs6666405	0.91[EUR][1000 genomes]
rs6667885	0.97[EUR][1000 genomes]
rs6669393	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6671005	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6671124	0.97[EUR][1000 genomes]
rs6688195	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs723334	0.90[EUR][1000 genomes]
rs732539	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7354865	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7412469	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs744096	0.96[EUR][1000 genomes]
rs7519866	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7532601	0.98[EUR][1000 genomes]
rs7541868	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7553243	0.91[EUR][1000 genomes]
rs8851	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs946320	0.91[EUR][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	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	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61782568	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL
rs61782568	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47157600-47172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:47158200-47172000	Weak transcription	Brain Angular Gyrus	brain
6	chr1:47159200-47182800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:47159400-47171200	Weak transcription	Right Ventricle	heart
8	chr1:47159400-47172200	Weak transcription	Psoas Muscle	Psoas
9	chr1:47160600-47173600	Strong transcription	Primary T cells from cord blood	blood
10	chr1:47160600-47174000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:47160600-47181200	Strong transcription	Dnd41	blood
12	chr1:47160800-47174000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:47160800-47175400	Strong transcription	Liver	Liver
14	chr1:47160800-47181800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:47160800-47182200	Strong transcription	Primary B cells from cord blood	blood
16	chr1:47160800-47182200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:47160800-47182400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:47160800-47182600	Strong transcription	Placenta	Placenta
19	chr1:47161000-47173400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:47161000-47173800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:47161200-47182200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:47161400-47182200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:47161400-47182800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:47164200-47173600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:47164200-47177400	Strong transcription	GM12878-XiMat	blood
26	chr1:47164400-47182200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:47164400-47182800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:47164600-47173400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:47164600-47181600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:47165600-47182200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:47166200-47182400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:47166400-47173800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:47166600-47173400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:47166600-47177200	Strong transcription	Fetal Brain Female	brain
35	chr1:47166600-47182400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:47166600-47182400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:47166600-47182800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr1:47166600-47182800	Strong transcription	Fetal Thymus	thymus
39	chr1:47166800-47172800	Strong transcription	Ovary	ovary
40	chr1:47166800-47173200	Strong transcription	Thymus	Thymus
41	chr1:47166800-47173400	Strong transcription	Brain Germinal Matrix	brain
42	chr1:47166800-47181800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:47166800-47182200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:47166800-47182400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:47166800-47182600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:47166800-47182800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:47167000-47173200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr1:47167000-47173200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr1:47167000-47174000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:47167000-47174400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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