Variant report

Variant	rs2900404
Chromosome Location	chr9:108663865-108663866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:108663819..108664519-chr9:108673345..108674675,3	MCF-7	breast:
2	chr9:108663733..108664585-chr9:109893673..109894313,2	MCF-7	breast:
3	chr9:108663816..108664349-chr9:108716067..108716712,2	MCF-7	breast:
4	chr9:108663460..108664528-chr9:108683360..108684140,3	MCF-7	breast:
5	chr9:108663745..108664473-chr9:109046470..109047272,2	MCF-7	breast:
6	chr9:108663424..108664248-chr9:108675232..108676055,3	MCF-7	breast:
7	chr9:108663748..108664564-chr9:108673596..108674358,3	MCF-7	breast:
8	chr9:108662761..108665200-chr9:108718437..108720079,2	MCF-7	breast:
9	chr9:108663616..108664421-chr9:109934294..109935106,2	K562	blood:
10	chr9:108663312..108664215-chr9:109410864..109411490,2	MCF-7	breast:
11	chr9:108663855..108664555-chr9:109048272..109049161,4	MCF-7	breast:
12	chr9:108660253..108666422-chr9:108715149..108718235,9	MCF-7	breast:
13	chr9:108663491..108664398-chr9:108979015..108980028,6	MCF-7	breast:
14	chr9:108662735..108665889-chr9:109622755..109626966,6	MCF-7	breast:
15	chr9:108663623..108664501-chr9:108675047..108675667,2	MCF-7	breast:
16	chr9:108663500..108664425-chr9:109934205..109935043,6	MCF-7	breast:
17	chr9:108663725..108664575-chr9:108674798..108675705,5	MCF-7	breast:
18	chr9:108658836..108662386-chr9:108662597..108665085,3	MCF-7	breast:
19	chr9:108663554..108664575-chr9:108674798..108675780,5	MCF-7	breast:
20	chr9:108663617..108664259-chr9:109085995..109086692,2	MCF-7	breast:
21	chr9:108663624..108664357-chr9:108675223..108675797,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000148143	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10115085	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117602	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10120538	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739215	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759148	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759149	0.81[EUR][1000 genomes]
rs10759150	0.81[EUR][1000 genomes]
rs10759151	0.81[EUR][1000 genomes]
rs10759152	0.81[EUR][1000 genomes]
rs10816352	0.99[ASN][1000 genomes]
rs10978330	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10978331	0.99[ASN][1000 genomes]
rs10978332	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978340	0.82[EUR][1000 genomes]
rs13296649	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16925032	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1987136	0.81[EUR][1000 genomes]
rs2417643	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417644	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417650	0.94[ASN][1000 genomes]
rs2417656	0.96[ASN][1000 genomes]
rs4598317	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742658	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742967	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742969	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742972	0.81[AMR][1000 genomes]
rs4742974	0.80[EUR][1000 genomes]
rs6477482	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025973	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040788	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7040794	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7043384	0.80[EUR][1000 genomes]
rs7044156	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7856876	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1041073	chr9:108535813-108731343	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1052684	chr9:108582944-108730280	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv615140	chr9:108592589-108725567	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv831679	chr9:108603112-108785347	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108662600-108664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:108662800-108664200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:108662800-108664200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:108663600-108664400	Enhancers	Right Ventricle	heart
5	chr9:108663600-108664600	Enhancers	Brain Cingulate Gyrus	brain
6	chr9:108663600-108664600	Enhancers	Brain Hippocampus Middle	brain
7	chr9:108663600-108664600	Enhancers	Fetal Heart	heart
8	chr9:108663600-108664800	Enhancers	Brain Substantia Nigra	brain
9	chr9:108663800-108664000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:108663800-108664200	Enhancers	Fetal Muscle Trunk	muscle

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