Variant report

Variant	rs5744106
Chromosome Location	chr1:223315969-223315970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr1:223315856-223316724	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAZ	chr1:223315756-223317534	K562	blood:	n/a	chr1:223316630-223316640
3	E2F6	chr1:223315846-223316860	K562	blood:	n/a	n/a
4	CTCF	chr1:223315900-223316050	HEEpiC	esophagus:	n/a	n/a
5	MAX	chr1:223315843-223317614	GM12878	blood:	n/a	chr1:223316630-223316640
6	POLR2A	chr1:223315837-223317506	K562	blood:	n/a	n/a
7	POLR2A	chr1:223315622-223317565	K562	blood:	n/a	n/a
8	TEAD4	chr1:223315902-223317619	K562	blood:	n/a	chr1:223316981-223316990
9	ZNF263	chr1:223315505-223317578	HEK293-T-REx	kidney:	n/a	chr1:223316428-223316437 chr1:223316429-223316450
10	MAX	chr1:223315959-223317007	ECC-1	luminal epithelium:	n/a	chr1:223316630-223316640
11	CTCF	chr1:223315898-223316878	HCT-116	colon:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
12	E2F6	chr1:223315633-223317591	K562	blood:	n/a	n/a
13	MAX	chr1:223315936-223316888	H1-hESC	embryonic stem cell:	n/a	chr1:223316630-223316640
14	TCF12	chr1:223315961-223316576	A549	lung:	n/a	n/a
15	CTCF	chr1:223315525-223317318	A549	lung:	n/a	chr1:223316368-223316384 chr1:223315736-223315743 chr1:223316172-223316185 chr1:223316457-223316470
16	RCOR1	chr1:223315948-223317737	K562	blood:	n/a	n/a
17	NR2F2	chr1:223315904-223317782	K562	blood:	n/a	n/a
18	CTCF	chr1:223315936-223316787	HCT-116	colon:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
19	MAX	chr1:223315964-223316889	H1-hESC	embryonic stem cell:	n/a	chr1:223316630-223316640
20	MAX	chr1:223315927-223317031	A549	lung:	n/a	chr1:223316630-223316640
21	SMARCB1	chr1:223315817-223316858	Hela-S3	cervix:	n/a	n/a
22	MAX	chr1:223315726-223317814	K562	blood:	n/a	chr1:223316630-223316640
23	CTCF	chr1:223315840-223315990	GM12874	blood:	n/a	n/a
24	CTCF	chr1:223315777-223316984	SK-N-SH	brain:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
25	MAX	chr1:223315913-223317103	HCT-116	colon:	n/a	chr1:223316630-223316640
26	POLR2A	chr1:223315298-223317592	GM12878	blood:	n/a	n/a
27	KAP1	chr1:223315634-223317095	HEK293	kidney:	n/a	n/a
28	MAX	chr1:223315766-223316990	K562	blood:	n/a	chr1:223316630-223316640
29	ZNF384	chr1:223315923-223316992	K562	blood:	n/a	n/a
30	SMC3	chr1:223315932-223316932	SK-N-SH	brain:	n/a	n/a
31	CBX3	chr1:223315847-223317626	K562	blood:	n/a	n/a
32	ZNF263	chr1:223315509-223316801	K562	blood:	n/a	chr1:223316428-223316437 chr1:223316429-223316450

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223305699..223307476-chr1:223314416..223316383,2	K562	blood:
2	chr1:223308071..223311101-chr1:223314181..223317156,4	K562	blood:

Variant related genes	Relation type
ENSG00000236846	TF binding region
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11488549	1.00[ASN][1000 genomes]
rs1341985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418143	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163741	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17163742	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs34088950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34970812	1.00[ASN][1000 genomes]
rs35705006	1.00[ASN][1000 genomes]
rs35802580	1.00[ASN][1000 genomes]
rs35953839	1.00[ASN][1000 genomes]
rs4393150	1.00[ASN][1000 genomes]
rs5744104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744144	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744151	1.00[MEX][hapmap]
rs5744156	0.90[EUR][1000 genomes]
rs61838985	1.00[ASN][1000 genomes]
rs67833495	1.00[ASN][1000 genomes]
rs72743840	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743860	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743869	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743871	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743874	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748469	0.86[EUR][1000 genomes]
rs72748471	0.86[EUR][1000 genomes]
rs72748472	0.86[EUR][1000 genomes]
rs72748475	0.86[EUR][1000 genomes]
rs72748482	0.90[EUR][1000 genomes]
rs73113934	1.00[ASN][1000 genomes]
rs73113935	1.00[ASN][1000 genomes]
rs73113941	1.00[ASN][1000 genomes]
rs73113948	1.00[ASN][1000 genomes]
rs988243	1.00[ASN][1000 genomes]
rs988244	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs988779	1.00[EUR][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	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223309400-223316000	Weak transcription	NHLF	lung
2	chr1:223310200-223316000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:223311200-223316000	Weak transcription	Liver	Liver
4	chr1:223311400-223316000	Weak transcription	Fetal Intestine Large	intestine
5	chr1:223311600-223316000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:223311600-223316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:223314000-223316000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:223314200-223316000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:223314200-223316000	Enhancers	Right Ventricle	heart
10	chr1:223314200-223316000	Enhancers	HSMMtube	muscle
11	chr1:223314400-223316000	Weak transcription	Psoas Muscle	Psoas
12	chr1:223314800-223316000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:223314800-223316000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:223314800-223316000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:223314800-223316000	Weak transcription	NH-A	brain
16	chr1:223314800-223316000	Enhancers	NHEK	skin
17	chr1:223314800-223316200	Enhancers	NHDF-Ad	bronchial
18	chr1:223314800-223316800	Active TSS	Brain Hippocampus Middle	brain
19	chr1:223315000-223316000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:223315200-223316000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:223315200-223316200	Enhancers	Spleen	Spleen
22	chr1:223315200-223317400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr1:223315200-223317600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:223315200-223318800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:223315400-223316000	Enhancers	Fetal Thymus	thymus
26	chr1:223315400-223316000	Bivalent Enhancer	GM12878-XiMat	blood
27	chr1:223315400-223316200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:223315400-223316200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:223315400-223316200	Weak transcription	Small Intestine	intestine
30	chr1:223315400-223316800	Active TSS	Brain Cingulate Gyrus	brain
31	chr1:223315400-223316800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr1:223315400-223318000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr1:223315600-223316000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr1:223315600-223316000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr1:223315600-223316000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:223315600-223316000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
37	chr1:223315600-223316000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:223315600-223316000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
39	chr1:223315600-223316000	Flanking Active TSS	Gastric	stomach
40	chr1:223315600-223316000	Flanking Active TSS	Lung	lung
41	chr1:223315600-223316200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:223315600-223316200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:223315600-223316200	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr1:223315600-223316400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr1:223315600-223316600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr1:223315600-223316800	Active TSS	Brain Substantia Nigra	brain
47	chr1:223315600-223316800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:223315600-223316800	Active TSS	Rectal Smooth Muscle	rectum
49	chr1:223315600-223317000	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr1:223315600-223317200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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