Variant report

Variant	rs3001453
Chromosome Location	chr9:96094327-96094328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96093481..96095896-chr9:96100994..96102832,2	MCF-7	breast:
2	chr9:96087091..96088640-chr9:96092305..96094945,2	MCF-7	breast:
3	chr9:96090542..96094852-chr9:96213032..96217839,6	MCF-7	breast:
4	chr9:96094285..96095889-chr9:96205467..96207499,2	MCF-7	breast:
5	chr9:96093858..96095483-chr9:96278870..96281860,2	MCF-7	breast:
6	chr9:96091189..96096083-chr9:96211395..96215893,15	MCF-7	breast:
7	chr9:96080130..96081909-chr9:96092886..96095724,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10739946	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10761208	0.83[GIH][hapmap]
rs1111776	0.83[GIH][hapmap]
rs12684392	0.83[GIH][hapmap]
rs1331588	0.83[TSI][hapmap]
rs1889338	1.00[CEU][hapmap]
rs1931372	0.81[EUR][1000 genomes]
rs2151714	1.00[CEU][hapmap]
rs2494781	0.95[EUR][1000 genomes]
rs28421070	1.00[EUR][1000 genomes]
rs2991376	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2991380	0.95[EUR][1000 genomes]
rs2991383	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2995993	1.00[EUR][1000 genomes]
rs2995994	0.95[EUR][1000 genomes]
rs2995999	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3001449	0.95[EUR][1000 genomes]
rs4548243	1.00[CEU][hapmap]
rs4743913	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4743914	0.90[EUR][1000 genomes]
rs4743916	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4743920	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4744229	0.81[EUR][1000 genomes]
rs6479479	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7020195	1.00[CEU][hapmap]
rs7025611	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7027660	0.90[EUR][1000 genomes]
rs999326	1.00[CEU][hapmap];0.83[YRI][hapmap]

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	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96068400-96100400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr9:96079600-96094400	Weak transcription	Stomach Mucosa	stomach
3	chr9:96081000-96100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96083200-96100400	Weak transcription	Fetal Stomach	stomach
5	chr9:96083400-96094400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:96083800-96094400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:96089200-96099400	Weak transcription	Fetal Brain Female	brain
8	chr9:96091400-96096400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:96092000-96096400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:96093200-96094800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:96093200-96095000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:96093400-96095600	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr9:96093400-96096200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr9:96093400-96096400	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr9:96094000-96095400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr9:96094000-96099800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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