Variant report

Variant	rs61782563
Chromosome Location	chr1:47158266-47158267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:47158180-47158330	BE2_C	brain:	n/a	n/a
2	CTCF	chr1:47158160-47158310	HAc	cerebellar:	n/a	n/a
3	CTCF	chr1:47158240-47158390	MCF-7	breast:	n/a	n/a
4	CTCF	chr1:47158120-47158270	HEEpiC	esophagus:	n/a	n/a
5	CTCF	chr1:47158180-47158330	HRE	kidney:	n/a	n/a
6	CTCF	chr1:47158180-47158330	HCFaa	heart:	n/a	n/a
7	CTCF	chr1:47158237-47158269	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:47158180-47158330	HVMF	connective:	n/a	n/a
9	CTCF	chr1:47158120-47158270	HFF-Myc	foreskin:	n/a	n/a
10	CTCF	chr1:47158160-47158310	SAEC	small airway:	n/a	n/a
11	CTCF	chr1:47158220-47158370	HEK293	kidney:	n/a	n/a
12	CTCF	chr1:47158180-47158330	NHLF	lung:	n/a	n/a
13	CTCF	chr1:47158120-47158270	AG04450	lung:	n/a	n/a
14	CTCF	chr1:47158260-47158410	HVMF	connective:	n/a	n/a
15	CTCF	chr1:47158220-47158370	NHEK	skin:	n/a	n/a
16	CTCF	chr1:47158140-47158290	AoAF	blood vessel:	n/a	n/a
17	CTCF	chr1:47158140-47158290	HCPEpiC	choroid plexus:	n/a	n/a
18	CTCF	chr1:47158200-47158350	RPTEC	kidney:	n/a	n/a
19	CTCF	chr1:47158169-47158299	HepG2	liver:	n/a	n/a
20	CTCF	chr1:47158180-47158330	HUVEC	blood vessel:	n/a	n/a
21	CTCF	chr1:47158160-47158310	HA-sp	spinal cord:	n/a	n/a
22	CTCF	chr1:47158160-47158310	HBMEC	blood vessel:	n/a	n/a
23	CTCF	chr1:47158200-47158350	Caco-2	colon:	n/a	n/a
24	CTCF	chr1:47158240-47158390	NHDF-neo	bronchial:	n/a	n/a
25	GATA3	chr1:47157642-47158289	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr1:47158120-47158270	AG10803	skin:	n/a	n/a
27	CTCF	chr1:47158180-47158330	HMF	breast:	n/a	n/a
28	CTCF	chr1:47158140-47158290	SAEC	small airway:	n/a	n/a
29	CTCF	chr1:47158060-47158422	IMR90	lung:	n/a	n/a
30	CTCF	chr1:47158212-47158290	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr1:47158120-47158270	BJ	skin:	n/a	n/a
32	CTCF	chr1:47158180-47158330	AG04449	skin:	n/a	n/a
33	CTCF	chr1:47158220-47158370	HCT-116	colon:	n/a	n/a
34	CTCF	chr1:47158180-47158330	HCPEpiC	choroid plexus:	n/a	n/a
35	CTCF	chr1:47158140-47158290	NHDF-neo	bronchial:	n/a	n/a
36	CTCF	chr1:47158220-47158370	HPF	lung:	n/a	n/a
37	CTCF	chr1:47158140-47158290	HepG2	liver:	n/a	n/a
38	CTCF	chr1:47158200-47158350	AG04450	lung:	n/a	n/a
39	CTCF	chr1:47158220-47158370	MCF-7	breast:	n/a	n/a
40	CTCF	chr1:47158220-47158370	HPAF	blood vessel:	n/a	n/a
41	CTCF	chr1:47158140-47158290	HRE	kidney:	n/a	n/a
42	CTCF	chr1:47158240-47158390	AoAF	blood vessel:	n/a	n/a
43	CTCF	chr1:47158160-47158310	AG09309	skin:	n/a	n/a
44	CTCF	chr1:47158120-47158270	HA-sp	spinal cord:	n/a	n/a
45	CTCF	chr1:47158140-47158290	AG10803	skin:	n/a	n/a
46	CTCF	chr1:47158140-47158290	AG09319	gingival:	n/a	n/a
47	CTCF	chr1:47158140-47158290	K562	blood:	n/a	n/a
48	CTCF	chr1:47158220-47158370	RPTEC	kidney:	n/a	n/a
49	CTCF	chr1:47158140-47158290	SK-N-SH_RA	brain:	n/a	n/a
50	CTCF	chr1:47158171-47158345	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47153374..47156939-chr1:47157123..47159935,3	K562	blood:
2	chr1:47148439..47150795-chr1:47155891..47158836,3	K562	blood:
3	chr1:47156029..47159013-chr1:47175919..47177585,2	K562	blood:
4	chr1:47157744..47160542-chr1:47181134..47183864,2	MCF-7	breast:

No data

Variant related genes	Relation type
EFCAB14	TF binding region
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10158678	0.97[EUR][1000 genomes]
rs10159351	0.97[EUR][1000 genomes]
rs1025806	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1048351	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048380	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075982	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10890411	0.97[EUR][1000 genomes]
rs11211338	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211341	0.93[EUR][1000 genomes]
rs11211344	0.97[EUR][1000 genomes]
rs11211346	0.94[EUR][1000 genomes]
rs1139758	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1150064	0.94[EUR][1000 genomes]
rs1150068	0.90[EUR][1000 genomes]
rs11801316	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11801419	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11804665	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12047537	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12078635	0.97[EUR][1000 genomes]
rs12082387	0.92[EUR][1000 genomes]
rs12094663	0.93[EUR][1000 genomes]
rs1258000	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1258002	0.81[EUR][1000 genomes]
rs1258003	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1258052	0.90[EUR][1000 genomes]
rs1258053	0.89[EUR][1000 genomes]
rs1258054	0.90[EUR][1000 genomes]
rs1258056	0.90[EUR][1000 genomes]
rs1258059	0.90[EUR][1000 genomes]
rs13417	0.94[EUR][1000 genomes]
rs1440486	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440489	0.87[EUR][1000 genomes]
rs17102352	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17102355	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17102473	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1745377	0.90[EUR][1000 genomes]
rs1933933	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1962900	0.96[EUR][1000 genomes]
rs2083486	0.97[EUR][1000 genomes]
rs2119301	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218189	0.97[EUR][1000 genomes]
rs2241862	0.94[EUR][1000 genomes]
rs2289446	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2289447	0.93[EUR][1000 genomes]
rs2304745	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405026	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405030	0.98[EUR][1000 genomes]
rs34932727	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737731	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766211	0.97[EUR][1000 genomes]
rs3766212	0.97[EUR][1000 genomes]
rs3766214	0.97[EUR][1000 genomes]
rs3766215	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766217	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766219	0.94[EUR][1000 genomes]
rs3766224	0.94[EUR][1000 genomes]
rs4272563	0.98[EUR][1000 genomes]
rs4274009	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4301586	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4443838	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55914029	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56319728	0.82[EUR][1000 genomes]
rs58185502	0.93[EUR][1000 genomes]
rs585257	0.94[EUR][1000 genomes]
rs594118	0.93[EUR][1000 genomes]
rs595813	0.93[EUR][1000 genomes]
rs59881815	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60173509	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60675294	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611468	0.93[EUR][1000 genomes]
rs614486	0.94[EUR][1000 genomes]
rs61782564	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782568	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61782590	0.86[EUR][1000 genomes]
rs61784001	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61784002	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61784003	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs618554	0.90[EUR][1000 genomes]
rs618878	0.80[EUR][1000 genomes]
rs620431	0.90[EUR][1000 genomes]
rs620913	0.90[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	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6429609	0.86[EUR][1000 genomes]
rs647999	0.88[EUR][1000 genomes]
rs6656244	0.88[ASN][1000 genomes]
rs6666405	0.90[EUR][1000 genomes]
rs6667885	0.96[EUR][1000 genomes]
rs6669393	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6671005	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6671124	0.97[EUR][1000 genomes]
rs6688195	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723334	0.91[EUR][1000 genomes]
rs732539	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7354865	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7412469	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744096	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7519866	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532601	0.97[EUR][1000 genomes]
rs7541868	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7553243	0.91[EUR][1000 genomes]
rs8851	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs946320	0.90[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
rs61782563	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL
rs61782563	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
2	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
5	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
7	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:47142000-47159400	Strong transcription	K562	blood
12	chr1:47142000-47159800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:47142600-47159200	Strong transcription	GM12878-XiMat	blood
14	chr1:47142600-47159400	Strong transcription	NHEK	skin
15	chr1:47142800-47158800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:47142800-47159600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:47142800-47159800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:47143200-47159400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:47143200-47159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:47143200-47159800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:47143600-47158400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:47143600-47159400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:47143800-47159400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:47143800-47159400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:47143800-47159800	Strong transcription	Primary T cells from cord blood	blood
26	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:47144600-47159600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:47145400-47159000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:47145800-47158800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:47147600-47158400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:47148400-47159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:47148800-47159400	Strong transcription	Hela-S3	cervix
33	chr1:47152200-47158800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:47153000-47159000	Strong transcription	Spleen	Spleen
35	chr1:47153200-47159400	Genic enhancers	Fetal Thymus	thymus
36	chr1:47153400-47159600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:47153600-47158400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:47153600-47159400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:47153600-47159600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:47153800-47158800	Strong transcription	Lung	lung
41	chr1:47154000-47158600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:47154000-47159400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:47154000-47159400	Strong transcription	Liver	Liver
44	chr1:47154000-47159800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:47154000-47159800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:47154000-47161000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:47154400-47158400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:47154600-47159200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:47155400-47158800	Genic enhancers	Thymus	Thymus

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