Variant report

Variant	rs59989465
Chromosome Location	chr2:99392025-99392026
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	TCF12	chr2:99391549-99392770	ECC-1	luminal epithelium:	n/a	chr2:99391964-99391973
2	USF1	chr2:99391588-99392460	ECC-1	luminal epithelium:	n/a	chr2:99391976-99391992
3	TEAD4	chr2:99391544-99392597	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr2:99391431-99392638	ECC-1	luminal epithelium:	n/a	chr2:99391511-99391520 chr2:99391857-99391868 chr2:99391853-99391872
5	ESR1	chr2:99391813-99392441	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr2:99391441-99392695	ECC-1	luminal epithelium:	n/a	n/a
7	FOXA1	chr2:99391696-99392387	ECC-1	luminal epithelium:	n/a	n/a
8	NFIC	chr2:99391439-99392735	ECC-1	luminal epithelium:	n/a	n/a
9	EP300	chr2:99391438-99392746	ECC-1	luminal epithelium:	n/a	chr2:99392305-99392314
10	FOXA1	chr2:99391755-99392325	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr2:99391540-99392504	ECC-1	luminal epithelium:	n/a	n/a
12	YY1	chr2:99391627-99392488	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr2:99391343-99392621	ECC-1	luminal epithelium:	n/a	chr2:99391511-99391520 chr2:99391857-99391868 chr2:99391853-99391872
14	CTCF	chr2:99391960-99392110	GM12873	blood:	n/a	n/a
15	TCF12	chr2:99391469-99392771	ECC-1	luminal epithelium:	n/a	chr2:99391964-99391973
16	CEBPB	chr2:99391633-99392519	ECC-1	luminal epithelium:	n/a	chr2:99391946-99391958
17	USF1	chr2:99391545-99392526	ECC-1	luminal epithelium:	n/a	chr2:99391976-99391992
18	FOXM1	chr2:99391587-99392585	ECC-1	luminal epithelium:	n/a	n/a
19	TEAD4	chr2:99391460-99392645	ECC-1	luminal epithelium:	n/a	n/a
20	NR3C1	chr2:99391566-99392555	ECC-1	luminal epithelium:	n/a	chr2:99391803-99391829 chr2:99391803-99391829 chr2:99391803-99391829 chr2:99391774-99391788 chr2:99391803-99391829 chr2:99391807-99391825
21	YY1	chr2:99391602-99392591	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr2:99391638-99392640	ECC-1	luminal epithelium:	n/a	chr2:99392305-99392314
23	ZBTB7A	chr2:99391803-99392573	ECC-1	luminal epithelium:	n/a	n/a
24	NR3C1	chr2:99391621-99392496	ECC-1	luminal epithelium:	n/a	chr2:99391803-99391829 chr2:99391803-99391829 chr2:99391803-99391829 chr2:99391774-99391788 chr2:99391803-99391829 chr2:99391807-99391825
25	ESR1	chr2:99391837-99392493	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99347124..99349184-chr2:99391953..99393526,2	MCF-7	breast:
2	chr2:99384290..99389208-chr2:99389339..99394045,5	MCF-7	breast:
3	chr2:99391796..99394293-chr2:99395311..99397641,2	MCF-7	breast:
4	chr2:99391084..99393411-chr2:99394844..99396426,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226791	TF binding region
ENSG00000226791	Chromatin interaction
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10496330	0.86[EUR][1000 genomes]
rs1877905	0.86[EUR][1000 genomes]
rs2090181	0.81[ASN][1000 genomes]
rs2203432	0.81[ASN][1000 genomes]
rs2871243	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2871244	0.81[ASN][1000 genomes]
rs3731660	0.94[ASN][1000 genomes]
rs4851160	0.81[ASN][1000 genomes]
rs57185248	0.87[ASN][1000 genomes]
rs58516468	0.87[ASN][1000 genomes]
rs58560917	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58676789	0.83[ASN][1000 genomes]
rs59083513	0.81[ASN][1000 genomes]
rs59313126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60496162	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61042973	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61311613	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61359279	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61402919	0.81[ASN][1000 genomes]
rs72811003	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72811004	0.91[ASN][1000 genomes]
rs72811005	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72825780	0.86[EUR][1000 genomes]
rs72825782	0.86[EUR][1000 genomes]
rs72825784	0.86[EUR][1000 genomes]
rs72825789	0.86[EUR][1000 genomes]
rs72825790	0.86[EUR][1000 genomes]
rs72825800	0.86[EUR][1000 genomes]
rs72825801	0.86[EUR][1000 genomes]
rs72827704	0.86[EUR][1000 genomes]
rs72827705	0.86[EUR][1000 genomes]
rs72827707	0.86[EUR][1000 genomes]
rs72827708	0.86[EUR][1000 genomes]
rs72827713	0.86[EUR][1000 genomes]
rs72827717	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72827722	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72827724	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72827726	0.87[ASN][1000 genomes]
rs72827727	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827728	0.84[ASN][1000 genomes]
rs72827729	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827731	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827733	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72827736	0.83[ASN][1000 genomes]
rs72827739	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72827740	0.81[ASN][1000 genomes]
rs72827741	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72827742	0.81[ASN][1000 genomes]
rs72827743	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99385800-99394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:99385800-99410400	Weak transcription	Right Atrium	heart
3	chr2:99388600-99392200	Weak transcription	Lung	lung
4	chr2:99389000-99392400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:99389000-99393000	Enhancers	Fetal Thymus	thymus
6	chr2:99389000-99393800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:99389200-99392400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:99389200-99392600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:99389400-99392600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr2:99389400-99392800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr2:99389600-99392200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:99390000-99392200	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr2:99391000-99393200	Enhancers	Fetal Brain Male	brain
14	chr2:99391000-99395400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:99391200-99393000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:99391400-99392200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr2:99391400-99392600	Enhancers	Esophagus	oesophagus
18	chr2:99391400-99392800	Enhancers	Pancreas	Pancrea
19	chr2:99391400-99393000	Enhancers	Fetal Muscle Leg	muscle
20	chr2:99391600-99392400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:99391600-99392400	Enhancers	NHEK	skin
22	chr2:99391600-99392600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:99391600-99392600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr2:99391600-99406600	Weak transcription	Thymus	Thymus
25	chr2:99391800-99392800	Enhancers	Brain Germinal Matrix	brain
26	chr2:99391800-99393000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:99391800-99393000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr2:99391800-99393000	Enhancers	HepG2	liver
29	chr2:99392000-99392200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:99392000-99392200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr2:99392000-99392200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr2:99392000-99392400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:99392000-99392400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr2:99392000-99392400	Flanking Active TSS	Fetal Brain Female	brain
35	chr2:99392000-99392600	Active TSS	Aorta	Aorta
36	chr2:99392000-99392600	Enhancers	Psoas Muscle	Psoas
37	chr2:99392000-99392800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:99392000-99393000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:99392000-99393000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:99392000-99393400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:99392000-99393400	Enhancers	Fetal Lung	lung

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