Variant report

Variant	rs5744105
Chromosome Location	chr1:223316077-223316078
allele	C/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	POLR2A	chr1:223316068-223317528	K562	blood:	n/a	n/a
3	EGR1	chr1:223316049-223316833	K562	blood:	n/a	chr1:223316663-223316677 chr1:223316176-223316189 chr1:223316630-223316640 chr1:223316647-223316657 chr1:223316667-223316676 chr1:223316629-223316643 chr1:223316179-223316189 chr1:223316633-223316643
4	MAZ	chr1:223315756-223317534	K562	blood:	n/a	chr1:223316630-223316640
5	E2F6	chr1:223315846-223316860	K562	blood:	n/a	n/a
6	E2F4	chr1:223316005-223316889	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr1:223316036-223317563	K562	blood:	n/a	chr1:223316630-223316640
8	POLR2A	chr1:223316045-223317035	SK-N-MC	brain:	n/a	n/a
9	MAX	chr1:223315978-223316931	MCF-7	breast:	n/a	chr1:223316630-223316640
10	MAX	chr1:223315843-223317614	GM12878	blood:	n/a	chr1:223316630-223316640
11	REST	chr1:223316073-223316591	K562	blood:	n/a	n/a
12	POLR2A	chr1:223315837-223317506	K562	blood:	n/a	n/a
13	POLR2A	chr1:223315622-223317565	K562	blood:	n/a	n/a
14	TEAD4	chr1:223315902-223317619	K562	blood:	n/a	chr1:223316981-223316990
15	E2F6	chr1:223315984-223316874	A549	lung:	n/a	n/a
16	HEY1	chr1:223316054-223316425	K562	blood:	n/a	chr1:223316348-223316363
17	ZNF263	chr1:223315505-223317578	HEK293-T-REx	kidney:	n/a	chr1:223316428-223316437 chr1:223316429-223316450
18	MAX	chr1:223315959-223317007	ECC-1	luminal epithelium:	n/a	chr1:223316630-223316640
19	CTCF	chr1:223315898-223316878	HCT-116	colon:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
20	CTCF	chr1:223316021-223316856	K562	blood:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
21	E2F6	chr1:223315633-223317591	K562	blood:	n/a	n/a
22	CTCF	chr1:223315987-223316748	MCF-7	breast:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
23	MAX	chr1:223315936-223316888	H1-hESC	embryonic stem cell:	n/a	chr1:223316630-223316640
24	TCF12	chr1:223315961-223316576	A549	lung:	n/a	n/a
25	CTCF	chr1:223315525-223317318	A549	lung:	n/a	chr1:223316368-223316384 chr1:223315736-223315743 chr1:223316172-223316185 chr1:223316457-223316470
26	ZBTB7A	chr1:223316062-223316709	ECC-1	luminal epithelium:	n/a	chr1:223316498-223316506
27	TBL1XR1	chr1:223316006-223316512	K562	blood:	n/a	n/a
28	RCOR1	chr1:223315948-223317737	K562	blood:	n/a	n/a
29	E2F6	chr1:223315994-223316478	H1-hESC	embryonic stem cell:	n/a	n/a
30	NR2F2	chr1:223315904-223317782	K562	blood:	n/a	n/a
31	UBTF	chr1:223316022-223317125	K562	blood:	n/a	n/a
32	MAX	chr1:223316063-223316520	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr1:223315936-223316787	HCT-116	colon:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
34	MAX	chr1:223315964-223316889	H1-hESC	embryonic stem cell:	n/a	chr1:223316630-223316640
35	MAX	chr1:223315927-223317031	A549	lung:	n/a	chr1:223316630-223316640
36	SMARCB1	chr1:223315817-223316858	Hela-S3	cervix:	n/a	n/a
37	MAX	chr1:223316014-223316924	ECC-1	luminal epithelium:	n/a	chr1:223316630-223316640
38	MAX	chr1:223315726-223317814	K562	blood:	n/a	chr1:223316630-223316640
39	POLR2A	chr1:223316030-223317607	K562	blood:	n/a	n/a
40	CTCF	chr1:223316026-223316930	K562	blood:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
41	TCF12	chr1:223316057-223316951	ECC-1	luminal epithelium:	n/a	n/a
42	MYC	chr1:223316015-223317516	K562	blood:	n/a	chr1:223316630-223316640
43	CTCF	chr1:223315777-223316984	SK-N-SH	brain:	n/a	chr1:223316368-223316384 chr1:223316172-223316185 chr1:223316457-223316470
44	MAX	chr1:223315913-223317103	HCT-116	colon:	n/a	chr1:223316630-223316640
45	MAX	chr1:223316067-223316883	A549	lung:	n/a	chr1:223316630-223316640
46	POLR2A	chr1:223315298-223317592	GM12878	blood:	n/a	n/a
47	KAP1	chr1:223315634-223317095	HEK293	kidney:	n/a	n/a
48	MAX	chr1:223315766-223316990	K562	blood:	n/a	chr1:223316630-223316640
49	SETDB1	chr1:223316063-223316571	K562	blood:	n/a	n/a
50	ZNF384	chr1:223315923-223316992	K562	blood:	n/a	n/a

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: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1341986	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1341987	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17661703	0.94[ASN][1000 genomes]
rs1773750	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1773755	0.95[ASN][1000 genomes]
rs1773756	0.94[ASN][1000 genomes]
rs1773757	0.94[ASN][1000 genomes]
rs1773758	0.95[ASN][1000 genomes]
rs2096141	0.91[ASN][1000 genomes]
rs2096142	0.91[ASN][1000 genomes]
rs2247421	0.95[ASN][1000 genomes]
rs2353475	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2353476	0.91[ASN][1000 genomes]
rs2353477	0.90[ASN][1000 genomes]
rs2487835	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2883182	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34849527	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35442320	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35511158	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5744113	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5744129	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61837568	0.92[ASN][1000 genomes]
rs61837569	0.92[ASN][1000 genomes]
rs61837573	0.92[ASN][1000 genomes]
rs61837574	0.92[ASN][1000 genomes]
rs61837575	0.92[ASN][1000 genomes]
rs61837577	0.91[ASN][1000 genomes]
rs723960	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72743865	0.92[ASN][1000 genomes]
rs851166	0.93[ASN][1000 genomes]
rs851171	0.92[ASN][1000 genomes]
rs9442047	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9442048	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975089	0.92[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	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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223311600-223316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:223314800-223316200	Enhancers	NHDF-Ad	bronchial
3	chr1:223314800-223316800	Active TSS	Brain Hippocampus Middle	brain
4	chr1:223315200-223316200	Enhancers	Spleen	Spleen
5	chr1:223315200-223317400	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr1:223315200-223317600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:223315200-223318800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:223315400-223316200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:223315400-223316200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:223315400-223316200	Weak transcription	Small Intestine	intestine
11	chr1:223315400-223316800	Active TSS	Brain Cingulate Gyrus	brain
12	chr1:223315400-223316800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr1:223315400-223318000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr1:223315600-223316200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:223315600-223316200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:223315600-223316200	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr1:223315600-223316400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr1:223315600-223316600	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:223315600-223316800	Active TSS	Brain Substantia Nigra	brain
20	chr1:223315600-223316800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:223315600-223316800	Active TSS	Rectal Smooth Muscle	rectum
22	chr1:223315600-223317000	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr1:223315600-223317200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr1:223315600-223317200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:223315600-223317600	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr1:223315800-223316200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:223315800-223316200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:223315800-223316200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr1:223315800-223316200	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr1:223315800-223316200	Flanking Active TSS	Fetal Brain Female	brain
31	chr1:223315800-223316200	Flanking Active TSS	Placenta	Placenta
32	chr1:223315800-223316200	Flanking Active TSS	Pancreas	Pancrea
33	chr1:223315800-223316200	Flanking Active TSS	K562	blood
34	chr1:223315800-223316400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
35	chr1:223315800-223316400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr1:223315800-223316400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:223315800-223316600	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:223315800-223316600	Active TSS	Brain Germinal Matrix	brain
39	chr1:223315800-223316600	Enhancers	Fetal Heart	heart
40	chr1:223315800-223316800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:223315800-223316800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:223315800-223316800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:223315800-223316800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
44	chr1:223315800-223316800	Active TSS	Brain Anterior Caudate	brain
45	chr1:223315800-223316800	Active TSS	Colonic Mucosa	Colon
46	chr1:223315800-223316800	Active TSS	Left Ventricle	heart
47	chr1:223315800-223317000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:223315800-223317000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:223315800-223317000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:223315800-223317000	Flanking Active TSS	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links