Variant report

Variant	rs2276604
Chromosome Location	chr2:99392745-99392746
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	TCF12	chr2:99391549-99392770	ECC-1	luminal epithelium:	n/a	chr2:99391964-99391973
2	EP300	chr2:99391438-99392746	ECC-1	luminal epithelium:	n/a	chr2:99392305-99392314
3	TCF12	chr2:99391469-99392771	ECC-1	luminal epithelium:	n/a	chr2:99391964-99391973

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: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10182043	0.84[EUR][1000 genomes]
rs10189330	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10202643	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs11123754	0.83[EUR][1000 genomes]
rs12712033	0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs12712035	0.83[JPT][hapmap]
rs12999225	0.87[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs13389386	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1356424	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1568213	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs17021941	0.85[EUR][1000 genomes]
rs1983352	0.84[JPT][hapmap]
rs2280142	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2280256	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs35929117	0.80[EUR][1000 genomes]
rs4263159	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6542837	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs6542838	0.85[JPT][hapmap]
rs6711022	0.82[ASN][1000 genomes]
rs6714330	0.81[EUR][1000 genomes]
rs6753465	0.82[EUR][1000 genomes]
rs6755640	0.83[EUR][1000 genomes]
rs6757099	0.87[ASN][1000 genomes]
rs7560696	0.84[CEU][hapmap]
rs7579189	0.85[JPT][hapmap]
rs7581128	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7582382	0.82[CHB][hapmap]
rs885115	0.83[EUR][1000 genomes]
rs981601	0.85[JPT][hapmap]
rs981602	0.81[CEU][hapmap];0.84[JPT][hapmap]

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:27 , 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	chr2:99389000-99393000	Enhancers	Fetal Thymus	thymus
4	chr2:99389000-99393800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:99389400-99392800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr2:99391000-99393200	Enhancers	Fetal Brain Male	brain
7	chr2:99391000-99395400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:99391200-99393000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:99391400-99392800	Enhancers	Pancreas	Pancrea
10	chr2:99391400-99393000	Enhancers	Fetal Muscle Leg	muscle
11	chr2:99391600-99406600	Weak transcription	Thymus	Thymus
12	chr2:99391800-99392800	Enhancers	Brain Germinal Matrix	brain
13	chr2:99391800-99393000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:99391800-99393000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:99391800-99393000	Enhancers	HepG2	liver
16	chr2:99392000-99392800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:99392000-99393000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:99392000-99393000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:99392000-99393400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:99392000-99393400	Enhancers	Fetal Lung	lung
21	chr2:99392200-99392800	Enhancers	Fetal Stomach	stomach
22	chr2:99392400-99393200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:99392400-99393200	Enhancers	Fetal Brain Female	brain
24	chr2:99392400-99393800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:99392600-99393000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:99392600-99393000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:99392600-99393000	Enhancers	Stomach Smooth Muscle	stomach

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