Variant report

Variant	rs7859727
Chromosome Location	chr9:22102165-22102166
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:22007684..22010358-chr9:22101724..22104831,4	MCF-7	breast:
2	chr9:21989926..21991515-chr9:22100273..22102679,2	MCF-7	breast:
3	chr9:21814593..21817244-chr9:22101346..22103643,2	MCF-7	breast:
4	chr9:22078947..22090885-chr9:22096375..22111093,52	MCF-7	breast:
5	chr9:22101484..22107036-chr9:22107375..22109985,6	MCF-7	breast:
6	chr9:22080093..22089919-chr9:22099951..22109614,29	MCF-7	breast:
7	chr9:22036364..22039051-chr9:22100287..22102911,2	MCF-7	breast:
8	chr9:22101148..22103535-chr9:22215387..22218852,3	MCF-7	breast:
9	chr9:22002808..22004535-chr9:22101357..22102863,2	MCF-7	breast:
10	chr9:22007811..22009878-chr9:22100767..22104347,3	MCF-7	breast:
11	chr9:22100911..22107878-chr9:22236967..22244514,15	MCF-7	breast:
12	chr9:21829244..21831745-chr9:22100291..22103460,3	MCF-7	breast:
13	chr9:21994077..21998286-chr9:22100828..22106631,7	MCF-7	breast:
14	chr9:21810090..21812748-chr9:22099940..22102610,2	MCF-7	breast:
15	chr9:21834703..21838145-chr9:22099294..22103119,4	MCF-7	breast:
16	chr9:22101600..22106273-chr9:22113482..22120974,11	MCF-7	breast:
17	chr9:22100284..22102861-chr9:22210891..22213800,3	MCF-7	breast:
18	chr9:22100896..22105456-chr9:22157698..22160659,5	MCF-7	breast:
19	chr9:21800490..21807994-chr9:22100829..22105470,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266446	Chromatin interaction
ENSG00000240498	Chromatin interaction
ENSG00000099810	Chromatin interaction
ENSG00000229298	Chromatin interaction
ENSG00000264545	Chromatin interaction
ENSG00000147889	Chromatin interaction
ENSG00000147883	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1004638	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10116277	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10217586	0.84[EUR][1000 genomes]
rs10511701	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10733376	0.92[EUR][1000 genomes]
rs10738606	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738608	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10738609	0.94[EUR][1000 genomes]
rs10738610	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs10757272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10757273	0.90[ASN][1000 genomes]
rs10757274	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10757275	0.97[EUR][1000 genomes]
rs10757277	0.91[EUR][1000 genomes]
rs10757278	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs10757279	0.91[EUR][1000 genomes]
rs10811654	0.94[EUR][1000 genomes]
rs10811656	0.88[EUR][1000 genomes]
rs1333042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1333043	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333046	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs1333047	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1333048	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs1333049	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs1412834	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1537370	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1537371	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537374	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1537375	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1537376	0.92[EUR][1000 genomes]
rs1556516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1970112	0.88[EUR][1000 genomes]
rs2210538	0.82[EUR][1000 genomes]
rs2383206	0.92[EUR][1000 genomes]
rs2383207	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2891168	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4977574	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4977575	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4977757	0.89[EUR][1000 genomes]
rs6475606	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6475609	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7022719	0.92[YRI][hapmap]
rs7341786	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7341791	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7857118	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7857345	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7859362	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs944797	0.92[EUR][1000 genomes]
rs9644860	0.81[EUR][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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22097200-22105400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:22097800-22102400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr9:22097800-22102600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:22097800-22105400	Weak transcription	Colonic Mucosa	Colon
5	chr9:22097800-22122400	Weak transcription	Dnd41	blood
6	chr9:22098000-22102200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:22098000-22102200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:22098000-22102200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:22098000-22104200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:22098000-22107600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:22099200-22102800	Weak transcription	Psoas Muscle	Psoas
12	chr9:22099400-22102200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:22099400-22102400	Weak transcription	Osteobl	bone
14	chr9:22099400-22102800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:22099400-22107200	Weak transcription	Small Intestine	intestine
16	chr9:22099600-22102400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:22099600-22102800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:22099600-22104000	Weak transcription	Adipose Nuclei	Adipose
19	chr9:22099800-22102400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:22099800-22102400	Weak transcription	Stomach Mucosa	stomach
21	chr9:22101600-22104400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:22101600-22109800	Enhancers	Fetal Intestine Large	intestine
23	chr9:22101600-22110000	Enhancers	Fetal Intestine Small	intestine
24	chr9:22101800-22102400	Enhancers	Hela-S3	cervix
25	chr9:22101800-22102600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:22101800-22102600	Bivalent Enhancer	GM12878-XiMat	blood
27	chr9:22101800-22103400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:22101800-22103600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:22101800-22104000	Enhancers	HSMMtube	muscle
30	chr9:22101800-22104200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr9:22101800-22104200	Enhancers	HSMM	muscle
32	chr9:22101800-22104400	Enhancers	Placenta	Placenta
33	chr9:22101800-22104600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr9:22101800-22104600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:22101800-22104600	Enhancers	NHEK	skin
36	chr9:22101800-22105200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr9:22101800-22105200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:22101800-22105600	Enhancers	NHDF-Ad	bronchial
39	chr9:22101800-22105800	Enhancers	HMEC	breast
40	chr9:22101800-22105800	Enhancers	NHLF	lung
41	chr9:22101800-22106000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr9:22101800-22106400	Enhancers	Duodenum Mucosa	Duodenum
43	chr9:22102000-22102400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:22102000-22103400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:22102000-22104600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:22102000-22105000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:22102000-22105400	Enhancers	NH-A	brain

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