Variant report

Variant	rs10821099
Chromosome Location	chr9:96013010-96013011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96005639..96009586-chr9:96012508..96016680,4	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10761201	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10761204	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10761205	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10761209	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821094	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10821096	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821100	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821101	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821105	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821106	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821107	0.91[CEU][hapmap];0.81[CHD][hapmap];0.90[TSI][hapmap]
rs10992689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992697	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992701	0.85[GIH][hapmap]
rs10992704	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1110335	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125029	0.84[MEX][hapmap]
rs12684394	0.85[EUR][1000 genomes]
rs1463544	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1889339	0.86[LWK][hapmap]
rs2012744	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2086103	0.85[EUR][1000 genomes]
rs3763634	0.86[EUR][1000 genomes]
rs3793546	0.84[EUR][1000 genomes]
rs41278286	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743905	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744203	0.86[EUR][1000 genomes]
rs4744207	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744215	0.90[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95995200-96026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:95995600-96030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:96001800-96018800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:96002600-96016400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:96005400-96033800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:96005600-96026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:96006200-96015200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:96006600-96014600	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:96007000-96014800	Weak transcription	Brain Substantia Nigra	brain
11	chr9:96007000-96020400	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:96007400-96015200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:96008000-96014400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr9:96008000-96030200	Strong transcription	Fetal Intestine Small	intestine
15	chr9:96008000-96030400	Strong transcription	Fetal Intestine Large	intestine
16	chr9:96008200-96026600	Weak transcription	Spleen	Spleen
17	chr9:96008200-96027600	Weak transcription	Right Atrium	heart
18	chr9:96008400-96014400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:96008400-96014600	Weak transcription	Hela-S3	cervix
20	chr9:96008400-96016600	Weak transcription	Gastric	stomach
21	chr9:96008800-96017200	Weak transcription	Brain Angular Gyrus	brain
22	chr9:96008800-96026200	Weak transcription	Placenta	Placenta
23	chr9:96009000-96014200	Weak transcription	Fetal Heart	heart
24	chr9:96010600-96014400	Weak transcription	Right Ventricle	heart
25	chr9:96010600-96016600	Weak transcription	Colonic Mucosa	Colon
26	chr9:96010800-96013800	Weak transcription	Fetal Thymus	thymus
27	chr9:96011000-96014200	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:96011000-96014400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:96011000-96014400	Weak transcription	Left Ventricle	heart
30	chr9:96011000-96014600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:96011000-96014800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:96011000-96015000	Weak transcription	Fetal Stomach	stomach
33	chr9:96011000-96016600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:96011000-96026400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr9:96011200-96015000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:96011200-96015200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:96011200-96017000	Weak transcription	Brain Anterior Caudate	brain
38	chr9:96011200-96017400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:96011200-96017600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:96011200-96018600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:96011200-96019400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:96011200-96030600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:96011200-96032800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:96011200-96033400	Weak transcription	A549	lung
45	chr9:96011400-96013800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:96011800-96014400	Weak transcription	Brain Germinal Matrix	brain
47	chr9:96011800-96026200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr9:96012400-96013400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:96012600-96019800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr9:96012800-96014000	Weak transcription	Stomach Smooth Muscle	stomach

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