Variant report

Variant	rs10116277
Chromosome Location	chr9:22081397-22081398
allele	G/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:21828987..21830849-chr9:22080193..22082601,3	MCF-7	breast:
2	chr9:21825303..21827537-chr9:22080207..22082765,2	MCF-7	breast:
3	chr9:22079101..22081952-chr9:22082169..22083681,2	MCF-7	breast:
4	chr9:21830900..21838533-chr9:22079723..22086252,27	MCF-7	breast:
5	chr9:22080093..22089919-chr9:22099951..22109614,29	MCF-7	breast:
6	chr9:21836576..21837111-chr9:22080830..22081499,2	MCF-7	breast:
7	chr9:22071994..22076005-chr9:22076573..22081529,4	MCF-7	breast:
8	chr9:22079850..22083849-chr9:22087242..22090618,5	MCF-7	breast:
9	chr9:21836749..21837521-chr9:22080759..22081467,5	MCF-7	breast:
10	chr9:22081254..22084984-chr9:22116484..22118588,4	MCF-7	breast:
11	chr9:22080679..22082945-chr9:22134850..22136541,2	MCF-7	breast:
12	chr9:22080912..22082747-chr9:22118308..22120981,2	MCF-7	breast:
13	chr9:22078947..22090885-chr9:22096375..22111093,52	MCF-7	breast:
14	chr9:21802949..21806302-chr9:22080908..22083994,4	MCF-7	breast:
15	chr9:21831674..21838507-chr9:22079741..22086703,33	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000099810	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1004638	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10511701	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs10733376	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10738606	0.86[EUR][1000 genomes]
rs10738607	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[EUR][1000 genomes]
rs10738608	0.82[EUR][1000 genomes]
rs10738609	0.82[EUR][1000 genomes]
rs10738610	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10757269	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10757271	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10757272	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[EUR][1000 genomes]
rs10757274	0.85[EUR][1000 genomes]
rs10757275	0.84[EUR][1000 genomes]
rs10757278	0.87[CEU][hapmap]
rs10811652	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10811654	0.81[EUR][1000 genomes]
rs1333040	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1333042	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1333043	0.93[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1333046	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1333047	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs1333048	0.96[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs1333049	0.89[CEU][hapmap]
rs1412832	0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs1412834	0.93[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1537370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537371	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1537373	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1537374	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1537375	0.82[EUR][1000 genomes]
rs1537376	0.83[EUR][1000 genomes]
rs1556516	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1970112	0.96[EUR][1000 genomes]
rs2383206	0.83[EUR][1000 genomes]
rs2383207	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2891168	1.00[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs4977574	1.00[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs4977575	0.89[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs6475606	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475609	0.85[EUR][1000 genomes]
rs7341786	0.89[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7341791	0.83[EUR][1000 genomes]
rs7857118	0.85[EUR][1000 genomes]
rs7857345	1.00[YRI][hapmap]
rs7859362	0.93[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7859727	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs944797	0.83[EUR][1000 genomes]
rs9632884	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9632885	0.84[AMR][1000 genomes];0.83[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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22073600-22084600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:22079000-22084600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:22080400-22083200	Weak transcription	NHEK	skin
4	chr9:22080400-22083800	Weak transcription	HSMMtube	muscle
5	chr9:22080400-22084000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:22080400-22084200	Weak transcription	NHDF-Ad	bronchial
7	chr9:22080400-22084400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:22080600-22083200	Weak transcription	Hela-S3	cervix
9	chr9:22080600-22083600	Weak transcription	NH-A	brain
10	chr9:22080600-22084000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:22080600-22084000	Weak transcription	NHLF	lung
12	chr9:22080600-22084400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:22080600-22089400	Weak transcription	Dnd41	blood
14	chr9:22080600-22098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:22080800-22081800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:22080800-22083000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:22080800-22083400	Weak transcription	HMEC	breast
18	chr9:22080800-22083800	Weak transcription	Osteobl	bone
19	chr9:22080800-22084000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:22080800-22084000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:22080800-22084400	Weak transcription	Aorta	Aorta
22	chr9:22080800-22084800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:22081000-22084000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:22081000-22084200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:22081000-22084400	Weak transcription	Adipose Nuclei	Adipose
26	chr9:22081200-22082400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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