Variant report

Variant	rs946320
Chromosome Location	chr1:47108343-47108344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47104425..47105991-chr1:47107497..47109430,2	K562	blood:
2	chr1:47108263..47110461-chr1:47134867..47136789,2	K562	blood:
3	chr1:47107881..47110216-chr1:47113427..47115932,2	K562	blood:
4	chr1:47101531..47103755-chr1:47107864..47109587,2	K562	blood:
5	chr1:47107701..47110694-chr1:47123742..47126591,2	MCF-7	breast:
6	chr1:47087818..47089652-chr1:47106481..47108594,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10158678	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10159351	0.93[EUR][1000 genomes]
rs1025806	0.90[EUR][1000 genomes]
rs1048351	0.90[EUR][1000 genomes]
rs1048380	0.88[EUR][1000 genomes]
rs1075982	0.94[EUR][1000 genomes]
rs10789492	0.80[EUR][1000 genomes]
rs10789493	0.80[EUR][1000 genomes]
rs10890411	0.93[EUR][1000 genomes]
rs10890416	0.82[EUR][1000 genomes]
rs11211338	0.92[EUR][1000 genomes]
rs11211341	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211344	0.93[EUR][1000 genomes]
rs11211346	0.88[EUR][1000 genomes]
rs11211354	0.80[EUR][1000 genomes]
rs1139758	0.94[EUR][1000 genomes]
rs1150064	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1150068	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11801316	0.91[EUR][1000 genomes]
rs11801419	0.86[EUR][1000 genomes]
rs11804665	0.94[EUR][1000 genomes]
rs12047537	0.94[EUR][1000 genomes]
rs12078635	0.93[EUR][1000 genomes]
rs12082387	0.86[EUR][1000 genomes]
rs12094663	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258000	0.84[EUR][1000 genomes]
rs1258002	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258004	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1258052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258059	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1440486	0.90[EUR][1000 genomes]
rs1440489	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17102352	0.94[EUR][1000 genomes]
rs17102355	0.94[EUR][1000 genomes]
rs17102473	0.87[EUR][1000 genomes]
rs1745377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933933	0.94[EUR][1000 genomes]
rs1962900	0.90[EUR][1000 genomes]
rs2083486	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2119301	0.91[EUR][1000 genomes]
rs2218189	0.93[EUR][1000 genomes]
rs2241862	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289446	0.94[EUR][1000 genomes]
rs2289447	0.91[EUR][1000 genomes]
rs2304745	0.91[EUR][1000 genomes]
rs2405026	0.90[EUR][1000 genomes]
rs2405030	0.92[EUR][1000 genomes]
rs34932727	0.90[EUR][1000 genomes]
rs3737731	0.90[EUR][1000 genomes]
rs3766211	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766212	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766214	0.93[EUR][1000 genomes]
rs3766215	0.91[EUR][1000 genomes]
rs3766217	0.90[EUR][1000 genomes]
rs3766219	0.96[EUR][1000 genomes]
rs3766224	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4272563	0.92[EUR][1000 genomes]
rs4274009	0.89[EUR][1000 genomes]
rs4301586	0.91[EUR][1000 genomes]
rs4443838	0.94[EUR][1000 genomes]
rs55914029	0.88[EUR][1000 genomes]
rs56319728	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58185502	0.91[EUR][1000 genomes]
rs585257	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs594118	0.97[EUR][1000 genomes]
rs595813	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59881815	0.94[EUR][1000 genomes]
rs60173509	0.94[EUR][1000 genomes]
rs60675294	0.91[EUR][1000 genomes]
rs611468	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614486	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61782563	0.90[EUR][1000 genomes]
rs61782564	0.90[EUR][1000 genomes]
rs61782568	0.91[EUR][1000 genomes]
rs61782590	0.80[EUR][1000 genomes]
rs61784001	0.94[EUR][1000 genomes]
rs61784002	0.94[EUR][1000 genomes]
rs61784003	0.92[EUR][1000 genomes]
rs618554	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618878	0.82[EUR][1000 genomes]
rs620431	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs620913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs625507	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs625590	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs637760	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs638845	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6429607	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6429608	0.84[EUR][1000 genomes]
rs6429609	0.87[EUR][1000 genomes]
rs6429610	0.81[EUR][1000 genomes]
rs647999	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6666405	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6667885	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6669393	0.94[EUR][1000 genomes]
rs6670495	0.81[EUR][1000 genomes]
rs6671005	0.90[EUR][1000 genomes]
rs6671124	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6688195	0.91[EUR][1000 genomes]
rs723334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723690	0.80[EUR][1000 genomes]
rs732539	0.92[EUR][1000 genomes]
rs7354865	0.91[EUR][1000 genomes]
rs7412469	0.91[EUR][1000 genomes]
rs744096	0.94[EUR][1000 genomes]
rs7519866	0.84[EUR][1000 genomes]
rs7532601	0.93[EUR][1000 genomes]
rs7534179	0.80[EUR][1000 genomes]
rs7541868	0.92[EUR][1000 genomes]
rs7553243	0.85[EUR][1000 genomes];0.81[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
rs946320	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL
rs946320	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:47083400-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:47088600-47108600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:47088600-47108800	Weak transcription	Hela-S3	cervix
6	chr1:47089800-47112400	Weak transcription	Small Intestine	intestine
7	chr1:47090200-47121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:47094600-47111000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:47094600-47119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:47095600-47109000	Strong transcription	Placenta	Placenta
11	chr1:47098200-47109000	Weak transcription	Esophagus	oesophagus
12	chr1:47098200-47113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:47098400-47112800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:47100000-47113400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:47101200-47109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:47101600-47108800	Weak transcription	GM12878-XiMat	blood
17	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:47101800-47108600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:47101800-47108800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:47101800-47109000	Weak transcription	Pancreas	Pancrea
22	chr1:47101800-47112400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:47101800-47112600	Weak transcription	Lung	lung
24	chr1:47101800-47112800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:47101800-47113000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:47101800-47115000	Weak transcription	Dnd41	blood
27	chr1:47101800-47115200	Weak transcription	Gastric	stomach
28	chr1:47101800-47119000	Weak transcription	Colonic Mucosa	Colon
29	chr1:47101800-47121200	Weak transcription	HUVEC	blood vessel
30	chr1:47102000-47108600	Weak transcription	NHDF-Ad	bronchial
31	chr1:47102000-47108600	Weak transcription	Osteobl	bone
32	chr1:47102000-47115000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:47102000-47122400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:47102400-47108800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr1:47102400-47121400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:47102800-47108800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:47102800-47108800	Weak transcription	HSMMtube	muscle
38	chr1:47103000-47108800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:47103000-47108800	Weak transcription	HSMM	muscle
40	chr1:47103000-47112800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:47103000-47115200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:47103000-47115200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
44	chr1:47103200-47113200	Weak transcription	Fetal Brain Female	brain
45	chr1:47103600-47108600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:47103800-47108600	Weak transcription	Thymus	Thymus
47	chr1:47103800-47108800	Weak transcription	Psoas Muscle	Psoas
48	chr1:47104000-47108800	Weak transcription	Right Ventricle	heart
49	chr1:47104000-47109000	Weak transcription	Aorta	Aorta
50	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach

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