Variant report

Variant	rs925884
Chromosome Location	chr2:99486419-99486420
allele	C/T
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	USF2	chr2:99486348-99486638	GM12878	blood:	n/a	chr2:99486481-99486492
6	TCF12	chr2:99485559-99486800	ECC-1	luminal epithelium:	n/a	chr2:99486350-99486360
7	CTCF	chr2:99486320-99486470	SAEC	small airway:	n/a	n/a
8	CTCF	chr2:99486280-99486430	SAEC	small airway:	n/a	n/a
9	MAX	chr2:99485624-99486876	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
10	POLR2A	chr2:99486345-99486450	MCF-7	breast:	n/a	n/a
11	POLR2A	chr2:99486186-99486732	ECC-1	luminal epithelium:	n/a	n/a
12	TCF7L2	chr2:99485733-99486703	Hela-S3	cervix:	n/a	n/a
13	MAX	chr2:99485646-99486771	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
14	CTCF	chr2:99486382-99486439	MCF-7	breast:	n/a	n/a
15	MAX	chr2:99485634-99486649	Hela-S3	cervix:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
16	EP300	chr2:99485677-99486844	ECC-1	luminal epithelium:	n/a	chr2:99485745-99485754 chr2:99486240-99486254
17	RFX5	chr2:99485476-99486905	Hela-S3	cervix:	n/a	chr2:99486633-99486641
18	CEBPB	chr2:99486205-99486804	MCF-7	breast:	n/a	n/a
19	EP300	chr2:99486242-99486840	T-47D	breast:	n/a	n/a
20	MYC	chr2:99486364-99486658	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
21	RFX5	chr2:99486226-99487287	SK-N-SH	brain:	n/a	chr2:99487133-99487142 chr2:99486633-99486641
22	HDAC2	chr2:99485396-99486857	MCF-7	breast:	n/a	n/a
23	GATA3	chr2:99486234-99486766	T-47D	breast:	n/a	chr2:99486511-99486523
24	EP300	chr2:99486308-99486681	T-47D	breast:	n/a	n/a
25	MAX	chr2:99485535-99486886	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
26	NFIC	chr2:99485582-99486976	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
27	RUNX3	chr2:99486126-99486451	GM12878	blood:	n/a	n/a
28	FOXA1	chr2:99486302-99486802	T-47D	breast:	n/a	n/a
29	ELF1	chr2:99485342-99486765	MCF-7	breast:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
30	CTCF	chr2:99486280-99486430	MCF-7	breast:	n/a	n/a
31	RCOR1	chr2:99485643-99486622	Hela-S3	cervix:	n/a	n/a
32	USF2	chr2:99485947-99486771	Hela-S3	cervix:	n/a	chr2:99486481-99486492
33	CTCF	chr2:99486280-99486430	HMEC	breast:	n/a	n/a
34	CEBPB	chr2:99485730-99486741	Hela-S3	cervix:	n/a	n/a
35	USF1	chr2:99486388-99486538	GM12878	blood:	n/a	n/a
36	SMC3	chr2:99485853-99486559	Hela-S3	cervix:	n/a	chr2:99486144-99486154 chr2:99486505-99486512
37	MAX	chr2:99485372-99486841	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
38	GATA3	chr2:99486317-99486718	MCF-7	breast:	n/a	chr2:99486511-99486523
39	TFAP2A	chr2:99485440-99486459	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr2:99486346-99486546	MCF10A-Er-Src	breast:	n/a	n/a
41	CREB1	chr2:99486380-99486766	ECC-1	luminal epithelium:	n/a	n/a
42	TEAD4	chr2:99485563-99486816	ECC-1	luminal epithelium:	n/a	n/a
43	USF1	chr2:99486115-99486830	ECC-1	luminal epithelium:	n/a	n/a
44	NFIC	chr2:99485503-99486914	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
45	FOXA1	chr2:99486391-99486846	T-47D	breast:	n/a	n/a
46	NR2F2	chr2:99485561-99486818	MCF-7	breast:	n/a	n/a
47	GATA3	chr2:99486242-99486767	T-47D	breast:	n/a	chr2:99486511-99486523
48	SRF	chr2:99485718-99486801	MCF-7	breast:	n/a	chr2:99486140-99486150
49	GATA3	chr2:99485440-99486871	MCF-7	breast:	n/a	chr2:99486511-99486523
50	ZNF143	chr2:99486385-99486731	Hela-S3	cervix:	n/a	n/a

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

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

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

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

rs_ID	r²[population]
rs1599956	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17021962	0.95[AMR][1000 genomes]
rs17022034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17022042	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022046	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022049	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4571099	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851164	0.80[CHB][hapmap]
rs4851165	0.80[CHB][hapmap]
rs4851168	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851169	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59878807	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66484268	0.93[ASN][1000 genomes]
rs67983743	0.93[ASN][1000 genomes]
rs72957614	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72958693	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs925883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs925885	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956166	0.95[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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99481800-99487000	Weak transcription	Lung	lung
2	chr2:99484000-99489000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:99484200-99486600	Flanking Active TSS	Hela-S3	cervix
4	chr2:99485000-99486800	Active TSS	Duodenum Mucosa	Duodenum
5	chr2:99485000-99488200	Enhancers	Fetal Muscle Leg	muscle
6	chr2:99485200-99487400	Weak transcription	Brain Angular Gyrus	brain
7	chr2:99485200-99487800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:99485400-99486600	Active TSS	Colonic Mucosa	Colon
9	chr2:99485400-99486600	Flanking Active TSS	Pancreas	Pancrea
10	chr2:99485400-99486800	Enhancers	Placenta	Placenta
11	chr2:99485400-99487400	Enhancers	Fetal Muscle Trunk	muscle
12	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:99485800-99486600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:99485800-99486800	Enhancers	GM12878-XiMat	blood
15	chr2:99485800-99487000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr2:99485800-99488200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:99485800-99491800	Weak transcription	Brain Anterior Caudate	brain
18	chr2:99486000-99486600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr2:99486000-99487600	Enhancers	Fetal Thymus	thymus
20	chr2:99486000-99488600	Weak transcription	Right Atrium	heart
21	chr2:99486200-99486600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr2:99486200-99486600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:99486200-99487000	Enhancers	HMEC	breast
24	chr2:99486200-99487600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:99486200-99487800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr2:99486200-99489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:99486400-99486600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:99486400-99486600	Enhancers	NHEK	skin
29	chr2:99486400-99486800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:99486400-99486800	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr2:99486400-99487000	Weak transcription	Gastric	stomach
32	chr2:99486400-99487200	Enhancers	Fetal Intestine Large	intestine
33	chr2:99486400-99487400	Enhancers	Fetal Intestine Small	intestine
34	chr2:99486400-99487800	Enhancers	Stomach Mucosa	stomach
35	chr2:99486400-99488000	Enhancers	Esophagus	oesophagus
36	chr2:99486400-99489600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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