Variant report

Variant	rs1440489
Chromosome Location	chr1:47126392-47126393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47126136..47128149-chr1:47129414..47131202,2	K562	blood:
2	chr1:47126136..47129004-chr1:47129301..47131202,4	K562	blood:
3	chr1:47124121..47126688-chr1:47131484..47133286,2	K562	blood:
4	chr1:47124455..47128063-chr1:47131072..47135010,3	MCF-7	breast:
5	chr1:47125032..47127467-chr1:47178869..47180403,2	K562	blood:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction
ENSG00000233647	Chromatin interaction
ENSG00000186118	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10158678	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10159351	0.88[EUR][1000 genomes]
rs1025806	0.87[EUR][1000 genomes]
rs1048351	0.86[EUR][1000 genomes]
rs1048380	0.85[EUR][1000 genomes]
rs1075982	0.85[EUR][1000 genomes]
rs10890411	0.88[EUR][1000 genomes]
rs11211338	0.87[EUR][1000 genomes]
rs11211341	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211344	0.88[EUR][1000 genomes]
rs11211346	0.85[EUR][1000 genomes]
rs1139758	0.86[EUR][1000 genomes]
rs1150064	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1150068	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11801316	0.88[EUR][1000 genomes]
rs11801419	0.94[EUR][1000 genomes]
rs11804665	0.86[EUR][1000 genomes]
rs12047537	0.85[EUR][1000 genomes]
rs12078635	0.88[EUR][1000 genomes]
rs12082387	0.83[EUR][1000 genomes]
rs12094663	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258002	0.82[EUR][1000 genomes]
rs1258052	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1258053	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1258054	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1258056	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1258059	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13417	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1440486	0.87[EUR][1000 genomes]
rs17102352	0.86[EUR][1000 genomes]
rs17102355	0.86[EUR][1000 genomes]
rs17102473	0.84[EUR][1000 genomes]
rs1745377	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1933933	0.85[EUR][1000 genomes]
rs1962900	0.89[EUR][1000 genomes]
rs2083486	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2119301	0.86[EUR][1000 genomes]
rs2218189	0.88[EUR][1000 genomes]
rs2241862	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289446	0.85[EUR][1000 genomes]
rs2289447	0.83[EUR][1000 genomes]
rs2304745	0.86[EUR][1000 genomes]
rs2405026	0.87[EUR][1000 genomes]
rs2405030	0.89[EUR][1000 genomes]
rs34932727	0.86[EUR][1000 genomes]
rs3737731	0.87[EUR][1000 genomes]
rs3766211	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766212	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766214	0.88[EUR][1000 genomes]
rs3766215	0.86[EUR][1000 genomes]
rs3766217	0.87[EUR][1000 genomes]
rs3766219	0.93[EUR][1000 genomes]
rs3766224	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4272563	0.89[EUR][1000 genomes]
rs4274009	0.86[EUR][1000 genomes]
rs4301586	0.88[EUR][1000 genomes]
rs4443838	0.85[EUR][1000 genomes]
rs55914029	0.84[EUR][1000 genomes]
rs56319728	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58185502	0.83[EUR][1000 genomes]
rs585257	0.87[EUR][1000 genomes]
rs594118	0.93[EUR][1000 genomes]
rs595813	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59881815	0.85[EUR][1000 genomes]
rs60173509	0.85[EUR][1000 genomes]
rs60675294	0.86[EUR][1000 genomes]
rs611468	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs614486	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61782563	0.87[EUR][1000 genomes]
rs61782564	0.87[EUR][1000 genomes]
rs61782568	0.86[EUR][1000 genomes]
rs61784001	0.85[EUR][1000 genomes]
rs61784002	0.85[EUR][1000 genomes]
rs61784003	0.87[EUR][1000 genomes]
rs618554	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618878	0.84[EUR][1000 genomes]
rs620431	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs620913	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs625507	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs625590	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs637760	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs638845	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6429607	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6429608	0.80[EUR][1000 genomes]
rs6429609	0.86[EUR][1000 genomes]
rs647999	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6666405	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6667885	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6669393	0.86[EUR][1000 genomes]
rs6671005	0.87[EUR][1000 genomes]
rs6671124	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6688195	0.86[EUR][1000 genomes]
rs723334	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs732539	0.87[EUR][1000 genomes]
rs7354865	0.88[EUR][1000 genomes]
rs7412469	0.86[EUR][1000 genomes]
rs744096	0.85[EUR][1000 genomes]
rs7519866	0.80[EUR][1000 genomes]
rs7532601	0.88[EUR][1000 genomes]
rs7541868	0.87[EUR][1000 genomes]
rs7553243	0.82[EUR][1000 genomes]
rs946320	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1440489	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL
rs1440489	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
5	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
6	chr1:47109400-47129800	Weak transcription	Pancreas	Pancrea
7	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
8	chr1:47109600-47132600	Weak transcription	HMEC	breast
9	chr1:47112400-47126800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:47115600-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:47115800-47132000	Weak transcription	Fetal Heart	heart
12	chr1:47116000-47127400	Weak transcription	Fetal Stomach	stomach
13	chr1:47116000-47130000	Weak transcription	Lung	lung
14	chr1:47116000-47130600	Weak transcription	Esophagus	oesophagus
15	chr1:47116000-47131800	Weak transcription	Aorta	Aorta
16	chr1:47116600-47130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:47116600-47131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:47117600-47127200	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:47117600-47127600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:47117600-47127600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:47117800-47126400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:47118000-47126600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:47118000-47126600	Strong transcription	Brain Anterior Caudate	brain
24	chr1:47118000-47132800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:47118200-47130000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:47119000-47132400	Weak transcription	A549	lung
27	chr1:47119200-47132400	Weak transcription	Small Intestine	intestine
28	chr1:47120000-47126400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:47120000-47127400	Weak transcription	Fetal Intestine Small	intestine
30	chr1:47121000-47126400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:47121000-47126600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:47121000-47129400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:47121000-47133000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:47122000-47129800	Weak transcription	Colonic Mucosa	Colon
35	chr1:47122000-47130000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:47122200-47130000	Weak transcription	NHEK	skin
37	chr1:47122200-47131000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:47122400-47132000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:47122600-47132200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:47122600-47133000	Weak transcription	Gastric	stomach
41	chr1:47122800-47129200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:47122800-47129400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:47122800-47129400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:47122800-47130000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:47122800-47130000	Weak transcription	Brain Germinal Matrix	brain
46	chr1:47122800-47130000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:47122800-47132000	Weak transcription	NHLF	lung
48	chr1:47122800-47132200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:47123000-47129800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:47123600-47129400	Weak transcription	Fetal Brain Female	brain

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