Variant report

Variant	rs618878
Chromosome Location	chr1:47144484-47144485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47141770..47144692-chr1:47177130..47178944,2	K562	blood:
2	chr1:47143526..47145109-chr1:47149868..47152359,2	MCF-7	breast:
3	chr1:47137606..47140204-chr1:47144038..47147459,3	K562	blood:
4	chr1:47141197..47146499-chr1:47148014..47152846,8	K562	blood:

Variant related genes	Relation type
ENSG00000228237	Chromatin interaction
ENSG00000159658	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10158678	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10159351	0.81[EUR][1000 genomes]
rs1025806	0.80[EUR][1000 genomes]
rs10890411	0.81[EUR][1000 genomes]
rs11211341	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11211344	0.81[EUR][1000 genomes]
rs1150064	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1150068	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12078635	0.81[EUR][1000 genomes]
rs12094663	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1258052	0.82[EUR][1000 genomes]
rs1258053	0.81[EUR][1000 genomes]
rs1258054	0.82[EUR][1000 genomes]
rs1258056	0.82[EUR][1000 genomes]
rs1258059	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13417	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1440486	0.80[EUR][1000 genomes]
rs1440489	0.84[EUR][1000 genomes]
rs1745377	0.82[EUR][1000 genomes]
rs2083486	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2218189	0.81[EUR][1000 genomes]
rs2241862	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2405026	0.80[EUR][1000 genomes]
rs2405030	0.82[EUR][1000 genomes]
rs3737731	0.80[EUR][1000 genomes]
rs3766211	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3766212	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3766214	0.81[EUR][1000 genomes]
rs3766217	0.80[EUR][1000 genomes]
rs3766219	0.86[EUR][1000 genomes]
rs3766224	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4272563	0.82[EUR][1000 genomes]
rs585257	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs594118	0.84[EUR][1000 genomes]
rs595813	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs611468	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs614486	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61782563	0.80[EUR][1000 genomes]
rs61782564	0.80[EUR][1000 genomes]
rs618554	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs620431	0.82[EUR][1000 genomes]
rs620913	0.82[EUR][1000 genomes]
rs625507	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs625590	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs637760	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs638845	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6429607	0.82[AMR][1000 genomes]
rs6666405	0.82[EUR][1000 genomes]
rs6667885	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6671005	0.80[EUR][1000 genomes]
rs6671124	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs723334	0.82[EUR][1000 genomes]
rs7532601	0.81[EUR][1000 genomes]
rs946320	0.82[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
rs618878	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL
rs618878	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47134400-47145800	Weak transcription	Hela-S3	cervix
2	chr1:47134400-47147800	Weak transcription	Small Intestine	intestine
3	chr1:47134600-47145600	Weak transcription	Fetal Kidney	kidney
4	chr1:47134600-47145800	Weak transcription	Fetal Brain Male	brain
5	chr1:47134600-47147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:47134600-47147800	Weak transcription	Psoas Muscle	Psoas
7	chr1:47134600-47149200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:47134600-47153000	Weak transcription	Right Atrium	heart
9	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:47134800-47152600	Weak transcription	A549	lung
11	chr1:47135000-47145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:47135000-47145400	Weak transcription	Esophagus	oesophagus
13	chr1:47138000-47152000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:47138000-47157800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:47138200-47147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:47138200-47152200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:47138200-47152600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
19	chr1:47138400-47147800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:47138400-47151600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr1:47138400-47152200	Strong transcription	Adipose Nuclei	Adipose
22	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:47138600-47152400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr1:47138800-47152800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:47138800-47153200	Strong transcription	Fetal Muscle Leg	muscle
27	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
28	chr1:47139000-47145800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:47139000-47148400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:47139000-47152400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:47139000-47152800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:47139200-47145200	Weak transcription	Gastric	stomach
34	chr1:47139200-47147400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:47139200-47153000	Weak transcription	Fetal Heart	heart
36	chr1:47139200-47153400	Strong transcription	Dnd41	blood
37	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
38	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:47139400-47146800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:47139400-47152600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:47139400-47152600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:47139400-47153000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:47139600-47152800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:47139600-47153000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:47139800-47147800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:47139800-47152800	Strong transcription	Osteobl	bone
49	chr1:47140000-47145400	Weak transcription	Colonic Mucosa	Colon
50	chr1:47140000-47155400	Strong transcription	HSMM	muscle

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