Variant report

Variant	rs57838764
Chromosome Location	chr3:50374568-50374569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:292)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:292 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr3:50374483-50375349	GM12878	blood:	n/a	n/a
2	MAX	chr3:50374199-50375883	NB4	blood:	n/a	n/a
3	TCF12	chr3:50374327-50375551	A549	lung:	n/a	n/a
4	MAZ	chr3:50374438-50375749	K562	blood:	n/a	n/a
5	POLR2A	chr3:50374156-50375497	HUVEC	blood vessel:	n/a	n/a
6	TCF3	chr3:50374258-50375568	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:50374026-50376674	K562	blood:	n/a	n/a
8	POLR2A	chr3:50374548-50375271	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:50374112-50375343	MCF10A-Er-Src	breast:	n/a	n/a
10	SIN3AK20	chr3:50374501-50374911	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:50374325-50375662	MCF-7	breast:	n/a	n/a
12	PAX5	chr3:50374354-50375199	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:50374056-50375219	Hela-S3	cervix:	n/a	n/a
14	E2F4	chr3:50373981-50375244	MCF10A-Er-Src	breast:	n/a	chr3:50375074-50375085
15	POLR2A	chr3:50374349-50375554	A549	lung:	n/a	n/a
16	POLR2A	chr3:50373760-50375545	Hela-S3	cervix:	n/a	n/a
17	POU2F2	chr3:50374558-50375752	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:50374095-50375796	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr3:50374429-50375555	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:50374483-50375364	A549	lung:	n/a	n/a
21	POLR2A	chr3:50372612-50375820	HL-60	blood:	n/a	n/a
22	SIN3A	chr3:50374029-50375727	GM12878	blood:	n/a	n/a
23	CCNT2	chr3:50374353-50375685	K562	blood:	n/a	n/a
24	FOXM1	chr3:50374501-50375800	GM12878	blood:	n/a	n/a
25	ZBTB7A	chr3:50374353-50374669	K562	blood:	n/a	n/a
26	POLR2A	chr3:50374402-50374966	A549	lung:	n/a	n/a
27	USF2	chr3:50374457-50375325	GM12878	blood:	n/a	n/a
28	MYC	chr3:50374527-50375164	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr3:50373947-50375754	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:50374236-50375766	GM15510	blood:	n/a	n/a
31	SP1	chr3:50374530-50375238	A549	lung:	n/a	chr3:50374931-50374942
32	POLR2A	chr3:50374033-50375836	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:50374331-50375829	K562	blood:	n/a	n/a
34	POLR2A	chr3:50374283-50375383	HepG2	liver:	n/a	n/a
35	MYBL2	chr3:50374516-50375506	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:50373521-50375529	Hela-S3	cervix:	n/a	n/a
37	ETS1	chr3:50374490-50374863	A549	lung:	n/a	n/a
38	POLR2A	chr3:50374462-50375339	U87	brain:	n/a	n/a
39	SIN3AK20	chr3:50374256-50375084	PANC-1	pancreas:	n/a	n/a
40	HDAC2	chr3:50374377-50374984	HepG2	liver:	n/a	n/a
41	MAX	chr3:50374199-50375649	HCT-116	colon:	n/a	n/a
42	NFIC	chr3:50374530-50374912	HepG2	liver:	n/a	n/a
43	MYC	chr3:50374538-50375245	HepG2	liver:	n/a	n/a
44	IRF1	chr3:50374279-50375138	K562	blood:	n/a	n/a
45	RFX5	chr3:50374552-50375673	GM12878	blood:	n/a	n/a
46	ELF1	chr3:50374369-50375165	K562	blood:	n/a	n/a
47	STAT1	chr3:50374344-50375236	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:50374174-50375837	K562	blood:	n/a	n/a
49	ZNF384	chr3:50374455-50374904	K562	blood:	n/a	n/a
50	ZNF263	chr3:50373836-50375398	HEK293-T-REx	kidney:	n/a	chr3:50374211-50374232

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50272229..50274587-chr3:50373396..50376334,2	MCF-7	breast:
2	chr3:50310332..50311966-chr3:50374071..50376123,2	MCF-7	breast:
3	chr3:50374237..50374856-chr7:5565993..5566639,2	Hela-S3	cervix:
4	chr3:50374544..50375354-chr9:3525800..3526347,2	NB4	blood:
5	chr3:50325622..50330493-chr3:50373581..50377874,6	K562	blood:
6	chr3:50373336..50376121-chr3:50395555..50398512,4	K562	blood:
7	chr3:50356822..50362778-chr3:50372728..50378128,10	MCF-7	breast:
8	chr3:50371739..50377775-chr3:50378206..50384768,10	MCF-7	breast:
9	chr3:50373346..50376603-chr3:50387024..50392661,8	MCF-7	breast:
10	chr3:50374257..50376540-chr3:50394477..50397107,2	MCF-7	breast:
11	chr3:50333907..50338508-chr3:50371973..50376030,7	K562	blood:
12	chr3:50372879..50374591-chr3:50450931..50453319,2	MCF-7	breast:
13	chr3:50373715..50376793-chr3:50377375..50380061,4	MCF-7	breast:
14	chr3:50329739..50332601-chr3:50372246..50375675,3	MCF-7	breast:
15	chr3:50335402..50338508-chr3:50371973..50376083,5	K562	blood:
16	chr3:50274751..50276271-chr3:50373939..50375555,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZMYND10-AS1	TF binding region
ENSG00000080298	Chromatin interaction
ENSG00000243477	Chromatin interaction
ENSG00000114395	Chromatin interaction
ENSG00000004838	Chromatin interaction
ENSG00000214706	Chromatin interaction
ENSG00000068001	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000126062	Chromatin interaction
ENSG00000272104	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000114388	Chromatin interaction
ENSG00000186792	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000235058	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12629572	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12635953	0.83[EUR][1000 genomes]
rs1989839	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071802	0.82[EUR][1000 genomes]
rs2071803	0.82[EUR][1000 genomes]
rs2073498	0.85[EUR][1000 genomes]
rs2073499	1.00[ASN][1000 genomes]
rs2233474	0.98[ASN][1000 genomes]
rs2236948	0.94[ASN][1000 genomes]
rs2236950	0.85[ASN][1000 genomes]
rs2236951	0.88[ASN][1000 genomes]
rs2239801	0.83[EUR][1000 genomes]
rs2282751	0.83[ASN][1000 genomes]
rs2301639	0.89[EUR][1000 genomes]
rs28365992	0.82[EUR][1000 genomes]
rs3213621	0.85[AFR][1000 genomes]
rs4141060	0.83[ASN][1000 genomes]
rs45536634	0.89[EUR][1000 genomes]
rs6776145	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs762705	0.89[ASN][1000 genomes]
rs9311449	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
10	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
13	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
14	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
16	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
17	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
18	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
19	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
20	nsv590258	chr3:50368278-50381022	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50372800-50375400	Active TSS	Right Ventricle	heart
2	chr3:50373000-50374600	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr3:50373200-50374600	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:50373200-50374800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr3:50373400-50374600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr3:50373400-50374600	Flanking Active TSS	Brain Angular Gyrus	brain
7	chr3:50373400-50375400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:50373400-50375800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:50373400-50375800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:50373600-50374600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:50373600-50375000	Active TSS	NHLF	lung
12	chr3:50373600-50375200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:50373600-50375200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:50373600-50375200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:50373600-50375200	Active TSS	Esophagus	oesophagus
16	chr3:50373600-50375400	Active TSS	Gastric	stomach
17	chr3:50373600-50375600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:50373600-50375600	Active TSS	Aorta	Aorta
19	chr3:50373600-50375600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:50373600-50375600	Active TSS	Lung	lung
21	chr3:50373600-50376000	Active TSS	GM12878-XiMat	blood
22	chr3:50373800-50374600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr3:50373800-50374600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
24	chr3:50373800-50374600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:50373800-50374800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr3:50373800-50375000	Active TSS	NHDF-Ad	bronchial
27	chr3:50373800-50375200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:50373800-50375200	Active TSS	Left Ventricle	heart
29	chr3:50373800-50375200	Active TSS	NHEK	skin
30	chr3:50373800-50375600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:50373800-50375600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr3:50373800-50375600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:50373800-50375600	Active TSS	HSMM	muscle
34	chr3:50373800-50375800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:50373800-50375800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:50373800-50375800	Active TSS	A549	lung
37	chr3:50373800-50379200	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr3:50374000-50375000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:50374000-50375000	Active TSS	HMEC	breast
40	chr3:50374000-50375000	Active TSS	HUVEC	blood vessel
41	chr3:50374000-50375000	Active TSS	NH-A	brain
42	chr3:50374000-50375200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:50374000-50375200	Active TSS	Muscle Satellite Cultured Cells	--
44	chr3:50374000-50375200	Active TSS	Hela-S3	cervix
45	chr3:50374000-50375400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:50374000-50375400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:50374000-50375400	Active TSS	HSMMtube	muscle
48	chr3:50374000-50375600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:50374000-50375600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:50374000-50375600	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links