Variant report

Variant	rs16912372
Chromosome Location	chr9:110079453-110079454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110045249..110048106-chr9:110077151..110079767,3	MCF-7	breast:
2	chr9:110070353..110073170-chr9:110078217..110082315,4	MCF-7	breast:
3	chr9:110044399..110049612-chr9:110071012..110080286,12	K562	blood:
4	chr9:110044605..110047075-chr9:110077754..110080578,5	MCF-7	breast:
5	chr9:110079426..110081266-chr9:110101654..110103447,2	MCF-7	breast:
6	chr9:110079143..110082107-chr9:110082961..110085070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10978789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10978793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11573631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11573652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11573655	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12001235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12001425	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12004883	1.00[CHB][hapmap]
rs12005299	0.93[EUR][1000 genomes]
rs12005522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17724694	0.97[EUR][1000 genomes]
rs56091145	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62567660	0.87[EUR][1000 genomes]
rs62567661	0.87[EUR][1000 genomes]
rs62567691	0.87[EUR][1000 genomes]
rs62567693	0.87[EUR][1000 genomes]
rs62567694	0.87[EUR][1000 genomes]
rs62567696	0.93[EUR][1000 genomes]
rs62567704	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62567738	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73668766	0.93[EUR][1000 genomes]
rs73668780	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7859324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.87[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	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	57 gene(s)	inside rSNPs	diseases
3	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
2	chr9:110061400-110094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:110064000-110085000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:110065200-110089200	Strong transcription	Fetal Thymus	thymus
5	chr9:110065600-110098600	Strong transcription	Dnd41	blood
6	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:110070400-110085000	Weak transcription	Colonic Mucosa	Colon
8	chr9:110070400-110099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:110071400-110084000	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:110071400-110103000	Weak transcription	Stomach Mucosa	stomach
11	chr9:110071800-110079800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:110071800-110084400	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:110073800-110080000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:110074200-110082600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:110074200-110083000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr9:110074200-110083200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:110074200-110088200	Strong transcription	Fetal Intestine Large	intestine
18	chr9:110075000-110080200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr9:110075000-110084800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:110075000-110088000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:110075200-110079600	Weak transcription	Aorta	Aorta
22	chr9:110075200-110084800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:110075200-110084800	Weak transcription	Spleen	Spleen
24	chr9:110075200-110090600	Weak transcription	Right Ventricle	heart
25	chr9:110075200-110093400	Weak transcription	Esophagus	oesophagus
26	chr9:110076000-110089400	Strong transcription	Primary hematopoietic stem cells	blood
27	chr9:110076200-110084600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:110076200-110087800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:110076400-110080600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:110076400-110084000	Weak transcription	Hela-S3	cervix
31	chr9:110076400-110084600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:110076800-110080400	Weak transcription	Lung	lung
33	chr9:110076800-110084200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:110076800-110084600	Weak transcription	Brain Substantia Nigra	brain
35	chr9:110076800-110088200	Weak transcription	Fetal Brain Male	brain
36	chr9:110077000-110079800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr9:110077000-110084400	Weak transcription	Fetal Brain Female	brain
38	chr9:110077200-110079600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr9:110077200-110080400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:110077200-110086200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:110077200-110090600	Weak transcription	Brain Germinal Matrix	brain
42	chr9:110077400-110080400	Weak transcription	HUVEC	blood vessel
43	chr9:110077400-110084000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr9:110077400-110084200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:110077600-110080400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr9:110077600-110080600	Weak transcription	Brain Anterior Caudate	brain
47	chr9:110077600-110093800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr9:110077800-110080200	Weak transcription	Adipose Nuclei	Adipose
49	chr9:110077800-110080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:110077800-110080400	Weak transcription	Fetal Kidney	kidney

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