Variant report

Variant	rs5744096
Chromosome Location	chr1:223317529-223317530
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	POLR2A	chr1:223316110-223317543	K562	blood:	n/a	n/a
2	TAL1	chr1:223316528-223317542	K562	blood:	n/a	n/a
3	MAZ	chr1:223315756-223317534	K562	blood:	n/a	chr1:223316630-223316640
4	EP300	chr1:223316628-223317614	GM12878	blood:	n/a	chr1:223317117-223317131
5	TCF3	chr1:223317230-223317545	GM12878	blood:	n/a	chr1:223317377-223317387
6	MAZ	chr1:223316084-223317968	GM12878	blood:	n/a	chr1:223316630-223316640
7	MYC	chr1:223316036-223317563	K562	blood:	n/a	chr1:223316630-223316640
8	CTCF	chr1:223317204-223317545	GM12878	blood:	n/a	n/a
9	MAX	chr1:223315843-223317614	GM12878	blood:	n/a	chr1:223316630-223316640
10	TBL1XR1	chr1:223317064-223317546	GM12878	blood:	n/a	n/a
11	HCFC1	chr1:223317253-223317581	K562	blood:	n/a	n/a
12	STAT1	chr1:223316562-223317631	GM12878	blood:	n/a	n/a
13	IRF1	chr1:223317122-223317531	K562	blood:	n/a	chr1:223317159-223317166
14	ZNF143	chr1:223316191-223317574	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:223317188-223317778	H1-neurons	neurons:	n/a	n/a
16	MEF2A	chr1:223316995-223317584	K562	blood:	n/a	chr1:223317291-223317306 chr1:223317292-223317306
17	POLR2A	chr1:223315622-223317565	K562	blood:	n/a	n/a
18	TEAD4	chr1:223315902-223317619	K562	blood:	n/a	chr1:223316981-223316990
19	POLR2A	chr1:223316201-223317550	K562	blood:	n/a	n/a
20	USF1	chr1:223317222-223317572	K562	blood:	n/a	n/a
21	ZNF263	chr1:223315505-223317578	HEK293-T-REx	kidney:	n/a	chr1:223316428-223316437 chr1:223316429-223316450
22	ELF1	chr1:223317069-223317546	K562	blood:	n/a	n/a
23	EP300	chr1:223316703-223317780	GM12878	blood:	n/a	chr1:223317117-223317131
24	E2F6	chr1:223317257-223317529	K562	blood:	n/a	n/a
25	E2F6	chr1:223315633-223317591	K562	blood:	n/a	n/a
26	NFIC	chr1:223316992-223317548	GM12878	blood:	n/a	n/a
27	RCOR1	chr1:223315948-223317737	K562	blood:	n/a	n/a
28	MTA3	chr1:223316725-223317539	GM12878	blood:	n/a	n/a
29	HEY1	chr1:223317103-223317545	K562	blood:	n/a	n/a
30	RUNX3	chr1:223316951-223317582	GM12878	blood:	n/a	n/a
31	E2F6	chr1:223317253-223317606	H1-hESC	embryonic stem cell:	n/a	n/a
32	NR2F2	chr1:223315904-223317782	K562	blood:	n/a	n/a
33	EBF1	chr1:223317031-223317558	GM12878	blood:	n/a	n/a
34	SP1	chr1:223317063-223317530	GM12878	blood:	n/a	chr1:223317340-223317352 chr1:223317337-223317351 chr1:223317341-223317351 chr1:223317341-223317350 chr1:223317342-223317351 chr1:223317341-223317351 chr1:223317340-223317352
35	MXI1	chr1:223316208-223317544	GM12878	blood:	n/a	n/a
36	EBF1	chr1:223316235-223317965	GM12878	blood:	n/a	n/a
37	MEF2C	chr1:223316991-223317609	GM12878	blood:	n/a	chr1:223317292-223317306 chr1:223317290-223317305
38	MAX	chr1:223315726-223317814	K562	blood:	n/a	chr1:223316630-223316640
39	MEF2A	chr1:223317057-223317575	GM12878	blood:	n/a	chr1:223317291-223317306 chr1:223317292-223317306
40	RCOR1	chr1:223316293-223317809	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:223316030-223317607	K562	blood:	n/a	n/a
42	WRNIP1	chr1:223316707-223317536	GM12878	blood:	n/a	n/a
43	BHLHE40	chr1:223316203-223317609	GM12878	blood:	n/a	n/a
44	CHD2	chr1:223316168-223317668	GM12878	blood:	n/a	n/a
45	E2F6	chr1:223317236-223317572	K562	blood:	n/a	n/a
46	EGR1	chr1:223317131-223317533	K562	blood:	n/a	n/a
47	POLR2A	chr1:223315298-223317592	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:223316474-223317646	K562	blood:	n/a	n/a
49	EP300	chr1:223316992-223317610	GM12878	blood:	n/a	chr1:223317117-223317131
50	CTCF	chr1:223317114-223317574	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223306168..223308719-chr1:223316086..223318176,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DISP1-2	chr1:223317391-223317585	XLOC_000579

Variant related genes	Relation type
TLR5	TF binding region
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1612431	1.00[AMR][1000 genomes]
rs1613248	1.00[AMR][1000 genomes]
rs1640804	1.00[AMR][1000 genomes]
rs1640806	1.00[AMR][1000 genomes]
rs1640807	1.00[AMR][1000 genomes]
rs1640808	1.00[AMR][1000 genomes]
rs1640862	1.00[AMR][1000 genomes]
rs1773735	1.00[AMR][1000 genomes]
rs1773740	1.00[AMR][1000 genomes]
rs1773741	1.00[AMR][1000 genomes]
rs1773742	1.00[AMR][1000 genomes]
rs1773743	1.00[AMR][1000 genomes]
rs1773745	1.00[AMR][1000 genomes]
rs1773746	1.00[AMR][1000 genomes]
rs1773747	1.00[AMR][1000 genomes]
rs1773748	1.00[AMR][1000 genomes]
rs5744098	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs725083	1.00[AMR][1000 genomes]
rs851159	1.00[AMR][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:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223315200-223317600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:223315200-223318800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr1:223315400-223318000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:223315600-223317600	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr1:223316000-223318200	Enhancers	Fetal Brain Male	brain
6	chr1:223316400-223317600	Flanking Active TSS	GM12878-XiMat	blood
7	chr1:223316400-223318200	Enhancers	Stomach Mucosa	stomach
8	chr1:223316600-223317600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr1:223316600-223317600	Flanking Active TSS	Fetal Heart	heart
10	chr1:223316600-223317800	Flanking Active TSS	Fetal Muscle Trunk	muscle
11	chr1:223316600-223317800	Enhancers	Gastric	stomach
12	chr1:223316600-223317800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:223316600-223318000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr1:223316600-223318000	Enhancers	Spleen	Spleen
15	chr1:223316800-223317600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr1:223316800-223317600	Flanking Active TSS	K562	blood
17	chr1:223316800-223317800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:223316800-223317800	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr1:223316800-223318000	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr1:223316800-223318000	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr1:223316800-223318000	Enhancers	Small Intestine	intestine
22	chr1:223316800-223318600	Enhancers	Lung	lung
23	chr1:223317000-223317600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:223317000-223317600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:223317000-223317600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:223317000-223317600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:223317000-223317600	Enhancers	Placenta	Placenta
28	chr1:223317000-223317600	Bivalent Enhancer	Fetal Stomach	stomach
29	chr1:223317000-223317600	Enhancers	Left Ventricle	heart
30	chr1:223317000-223317800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:223317000-223317800	Enhancers	Brain Cingulate Gyrus	brain
32	chr1:223317000-223317800	Enhancers	HSMMtube	muscle
33	chr1:223317000-223318000	Enhancers	Primary B cells from peripheral blood	blood
34	chr1:223317000-223318000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:223317000-223318000	Enhancers	Brain Germinal Matrix	brain
36	chr1:223317000-223318000	Enhancers	Esophagus	oesophagus
37	chr1:223317000-223318000	Enhancers	Pancreas	Pancrea
38	chr1:223317000-223318200	Enhancers	Right Ventricle	heart
39	chr1:223317000-223318400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:223317000-223318400	Enhancers	Fetal Intestine Large	intestine
41	chr1:223317000-223318400	Enhancers	Fetal Intestine Small	intestine
42	chr1:223317000-223318600	Enhancers	Fetal Muscle Leg	muscle
43	chr1:223317000-223318600	Enhancers	Fetal Thymus	thymus
44	chr1:223317200-223317600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:223317200-223317600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr1:223317200-223317600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:223317200-223317600	Enhancers	Brain Anterior Caudate	brain
48	chr1:223317200-223317600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr1:223317200-223317600	Enhancers	HSMM	muscle
50	chr1:223317200-223317800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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