Variant report

Variant	rs4399765
Chromosome Location	chr2:47601257-47601258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr2:47600774-47601306	HepG2	liver:	n/a	n/a
2	SMC3	chr2:47600956-47601261	K562	blood:	n/a	n/a
3	CTCF	chr2:47600872-47601334	A549	lung:	n/a	n/a
4	SMC3	chr2:47600883-47601291	HepG2	liver:	n/a	n/a
5	RFX5	chr2:47601185-47601340	K562	blood:	n/a	n/a
6	RAD21	chr2:47600799-47601404	HepG2	liver:	n/a	n/a
7	CTCF	chr2:47600827-47601336	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr2:47600715-47601550	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr2:47600877-47601264	SK-N-SH_RA	brain:	n/a	n/a
10	RAD21	chr2:47600854-47601278	MCF-7	breast:	n/a	n/a
11	CTCF	chr2:47600924-47601259	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr2:47601120-47601270	BE2_C	brain:	n/a	n/a
13	MAX	chr2:47600793-47601384	HepG2	liver:	n/a	chr2:47601102-47601112
14	RAD21	chr2:47600893-47601301	HepG2	liver:	n/a	n/a
15	ARID3A	chr2:47600972-47601258	HepG2	liver:	n/a	chr2:47601231-47601247 chr2:47601232-47601248
16	CTCF	chr2:47600572-47601471	A549	lung:	n/a	n/a
17	RAD21	chr2:47600777-47601357	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr2:47600868-47601303	K562	blood:	n/a	n/a
19	CTCF	chr2:47601160-47601310	GM06990	blood:	n/a	n/a
20	ZNF143	chr2:47601054-47601323	K562	blood:	n/a	n/a
21	RAD21	chr2:47600881-47601278	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYBL2	chr2:47600760-47601343	HepG2	liver:	n/a	n/a
23	RAD21	chr2:47600811-47601383	A549	lung:	n/a	n/a
24	RAD21	chr2:47600747-47601270	HCT-116	colon:	n/a	n/a
25	CTCF	chr2:47601000-47601270	A549	lung:	n/a	n/a
26	BHLHE40	chr2:47600966-47601276	HepG2	liver:	n/a	n/a
27	RAD21	chr2:47600861-47601328	SK-N-SH_RA	brain:	n/a	n/a
28	SMC3	chr2:47600764-47601422	SK-N-SH	brain:	n/a	n/a
29	RAD21	chr2:47600910-47601340	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47601008..47603575-chr2:47604857..47606633,2	K562	blood:
2	chr2:47559485..47574826-chr2:47594341..47605593,65	MCF-7	breast:

No data

Variant related genes	Relation type
MIR559	TF binding region
ENSG00000119888	Chromatin interaction
ENSG00000234690	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17036537	0.88[ASN][1000 genomes]
rs17036544	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35079997	0.98[ASN][1000 genomes]
rs3923560	0.95[ASN][1000 genomes]
rs4953497	0.96[ASN][1000 genomes]
rs55931899	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56368712	0.95[ASN][1000 genomes]
rs59327755	0.86[EUR][1000 genomes]
rs60417954	0.93[ASN][1000 genomes]
rs61348463	0.93[ASN][1000 genomes]
rs61493074	0.93[ASN][1000 genomes]
rs62138459	0.88[ASN][1000 genomes]
rs66617176	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72808422	0.88[ASN][1000 genomes]
rs72810397	0.87[ASN][1000 genomes]
rs72812303	0.84[AFR][1000 genomes]
rs72812306	0.93[ASN][1000 genomes]
rs72812307	0.93[ASN][1000 genomes]
rs7608471	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1009586	chr2:47552706-47621487	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47597200-47610600	Weak transcription	Right Atrium	heart
2	chr2:47597200-47615000	Weak transcription	Esophagus	oesophagus
3	chr2:47597200-47619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:47597400-47602600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:47597400-47604000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:47597400-47607000	Weak transcription	Gastric	stomach
7	chr2:47597400-47614800	Weak transcription	HMEC	breast
8	chr2:47597400-47617000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:47597400-47629400	Weak transcription	NHEK	skin
10	chr2:47597600-47615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:47598400-47603400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:47598400-47604200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:47598600-47601600	Weak transcription	Fetal Brain Male	brain
14	chr2:47598600-47604200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:47598600-47607000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:47598600-47607000	Weak transcription	Pancreas	Pancrea
17	chr2:47598600-47607200	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:47598600-47613000	Weak transcription	Lung	lung
19	chr2:47599000-47601400	Active TSS	Fetal Intestine Large	intestine
20	chr2:47599000-47606200	Weak transcription	Fetal Kidney	kidney
21	chr2:47599200-47608000	Weak transcription	Fetal Stomach	stomach
22	chr2:47599400-47601400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
23	chr2:47599400-47602400	Weak transcription	K562	blood
24	chr2:47599400-47603800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:47600000-47602800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:47600200-47617800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:47600400-47616800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:47600600-47601400	Enhancers	Fetal Lung	lung
29	chr2:47600600-47614000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:47600600-47617200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:47600800-47601400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:47600800-47601800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
33	chr2:47600800-47614000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:47601000-47601600	Weak transcription	HepG2	liver
35	chr2:47601000-47604200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:47601000-47610200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr2:47601000-47610600	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr2:47601000-47614200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:47601200-47601400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
40	chr2:47601200-47601600	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr2:47601200-47602000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
42	chr2:47601200-47604400	Weak transcription	Colonic Mucosa	Colon
43	chr2:47601200-47609400	Weak transcription	Brain Anterior Caudate	brain
44	chr2:47601200-47614600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:47601200-47616800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:47601200-47629400	Weak transcription	Stomach Mucosa	stomach

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