Variant report

Variant	rs925885
Chromosome Location	chr2:99486146-99486147
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	ELF1	chr2:99485380-99486856	MCF-7	breast:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
2	POLR2A	chr2:99485671-99486713	Hela-S3	cervix:	n/a	n/a
3	GTF2F1	chr2:99485663-99486572	Hela-S3	cervix:	n/a	n/a
4	USF1	chr2:99485823-99486723	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr2:99485424-99486309	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr2:99485559-99486800	ECC-1	luminal epithelium:	n/a	chr2:99486350-99486360
7	POLR2A	chr2:99485534-99486172	MCF-7	breast:	n/a	n/a
8	MAX	chr2:99485624-99486876	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
9	TCF7L2	chr2:99485733-99486703	Hela-S3	cervix:	n/a	n/a
10	MAX	chr2:99485646-99486771	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
11	STAT3	chr2:99485940-99486189	MCF10A-Er-Src	breast:	n/a	n/a
12	MAX	chr2:99485634-99486649	Hela-S3	cervix:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
13	EP300	chr2:99485677-99486844	ECC-1	luminal epithelium:	n/a	chr2:99485745-99485754 chr2:99486240-99486254
14	RFX5	chr2:99485476-99486905	Hela-S3	cervix:	n/a	chr2:99486633-99486641
15	MYC	chr2:99486136-99486162	MCF-7	breast:	n/a	n/a
16	HDAC2	chr2:99485396-99486857	MCF-7	breast:	n/a	n/a
17	MXI1	chr2:99485692-99486149	Hela-S3	cervix:	n/a	n/a
18	MAX	chr2:99485535-99486886	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
19	NFIC	chr2:99485582-99486976	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
20	RUNX3	chr2:99486126-99486451	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:99486007-99486246	Hela-S3	cervix:	n/a	n/a
22	ELF1	chr2:99485342-99486765	MCF-7	breast:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
23	RCOR1	chr2:99485643-99486622	Hela-S3	cervix:	n/a	n/a
24	USF2	chr2:99485947-99486771	Hela-S3	cervix:	n/a	chr2:99486481-99486492
25	FOXA1	chr2:99485679-99486147	T-47D	breast:	n/a	n/a
26	STAT3	chr2:99485826-99486225	MCF10A-Er-Src	breast:	n/a	n/a
27	CEBPB	chr2:99485730-99486741	Hela-S3	cervix:	n/a	n/a
28	SMC3	chr2:99485853-99486559	Hela-S3	cervix:	n/a	chr2:99486144-99486154 chr2:99486505-99486512
29	MAX	chr2:99485372-99486841	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
30	TFAP2A	chr2:99485440-99486459	Hela-S3	cervix:	n/a	n/a
31	TEAD4	chr2:99485563-99486816	ECC-1	luminal epithelium:	n/a	n/a
32	USF1	chr2:99486115-99486830	ECC-1	luminal epithelium:	n/a	n/a
33	NFIC	chr2:99485503-99486914	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
34	MYC	chr2:99485730-99486179	MCF10A-Er-Src	breast:	n/a	n/a
35	NR2F2	chr2:99485561-99486818	MCF-7	breast:	n/a	n/a
36	SRF	chr2:99485718-99486801	MCF-7	breast:	n/a	chr2:99486140-99486150
37	GATA3	chr2:99485440-99486871	MCF-7	breast:	n/a	chr2:99486511-99486523
38	SIN3AK20	chr2:99484869-99487036	MCF-7	breast:	n/a	n/a
39	YY1	chr2:99485639-99486203	ECC-1	luminal epithelium:	n/a	n/a
40	GATA3	chr2:99485632-99486870	MCF-7	breast:	n/a	chr2:99486511-99486523
41	TCF12	chr2:99485436-99486934	ECC-1	luminal epithelium:	n/a	chr2:99486350-99486360
42	TFAP2C	chr2:99485377-99486572	Hela-S3	cervix:	n/a	n/a
43	ZNF217	chr2:99485484-99486759	MCF-7	breast:	n/a	n/a
44	TEAD4	chr2:99485611-99486264	ECC-1	luminal epithelium:	n/a	n/a
45	MYC	chr2:99485821-99486197	MCF10A-Er-Src	breast:	n/a	n/a
46	NR2F2	chr2:99484910-99486778	MCF-7	breast:	n/a	n/a
47	POLR2A	chr2:99485457-99486160	MCF-7	breast:	n/a	n/a
48	POLR2A	chr2:99485534-99486498	Hela-S3	cervix:	n/a	n/a
49	MAZ	chr2:99485370-99486174	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99223862..99225617-chr2:99483733..99486358,2	MCF-7	breast:
2	chr2:99485026..99487433-chr2:100105196..100107704,3	MCF-7	breast:
3	chr2:99484412..99487919-chr2:99523957..99528531,6	MCF-7	breast:

Variant related genes	Relation type
KIAA1211L	TF binding region
ENSG00000196872	Chromatin interaction
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1599956	0.95[AMR][1000 genomes]
rs17021962	0.92[AMR][1000 genomes]
rs17022034	0.93[ASN][1000 genomes]
rs17022042	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17022046	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17022049	0.95[AMR][1000 genomes]
rs4571099	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4851168	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4851169	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59878807	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66484268	0.93[ASN][1000 genomes]
rs67983743	0.93[ASN][1000 genomes]
rs72957614	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72958693	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs925883	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs925884	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956166	0.92[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99481400-99486400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:99481400-99486400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:99481800-99487000	Weak transcription	Lung	lung
4	chr2:99484000-99489000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:99484200-99486600	Flanking Active TSS	Hela-S3	cervix
6	chr2:99484600-99486200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:99484600-99486400	Flanking Active TSS	NHEK	skin
8	chr2:99484800-99486200	Active TSS	Esophagus	oesophagus
9	chr2:99484800-99486200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:99484800-99486400	Flanking Active TSS	Fetal Intestine Large	intestine
11	chr2:99485000-99486200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:99485000-99486200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:99485000-99486400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:99485000-99486400	Active TSS	Rectal Smooth Muscle	rectum
15	chr2:99485000-99486800	Active TSS	Duodenum Mucosa	Duodenum
16	chr2:99485000-99488200	Enhancers	Fetal Muscle Leg	muscle
17	chr2:99485200-99486200	Flanking Active TSS	HMEC	breast
18	chr2:99485200-99487400	Weak transcription	Brain Angular Gyrus	brain
19	chr2:99485200-99487800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:99485400-99486200	Flanking Bivalent TSS/Enh	HepG2	liver
21	chr2:99485400-99486400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr2:99485400-99486400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:99485400-99486400	Flanking Active TSS	Fetal Intestine Small	intestine
24	chr2:99485400-99486400	Active TSS	Gastric	stomach
25	chr2:99485400-99486600	Active TSS	Colonic Mucosa	Colon
26	chr2:99485400-99486600	Flanking Active TSS	Pancreas	Pancrea
27	chr2:99485400-99486800	Enhancers	Placenta	Placenta
28	chr2:99485400-99487400	Enhancers	Fetal Muscle Trunk	muscle
29	chr2:99485600-99486400	Active TSS	Stomach Mucosa	stomach
30	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:99485800-99486200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:99485800-99486600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr2:99485800-99486800	Enhancers	GM12878-XiMat	blood
34	chr2:99485800-99487000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr2:99485800-99488200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:99485800-99491800	Weak transcription	Brain Anterior Caudate	brain
37	chr2:99486000-99486200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr2:99486000-99486200	Enhancers	HSMM	muscle
39	chr2:99486000-99486400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr2:99486000-99486600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr2:99486000-99487600	Enhancers	Fetal Thymus	thymus
42	chr2:99486000-99488600	Weak transcription	Right Atrium	heart

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