Variant report

Variant	rs2779772
Chromosome Location	chr9:17147191-17147192
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10115784	0.96[YRI][hapmap]
rs10511633	1.00[ASW][hapmap];0.80[CEU][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10962886	0.81[CEU][hapmap]
rs10962904	0.81[CEU][hapmap]
rs10962909	0.88[AMR][1000 genomes]
rs10962941	0.86[ASW][hapmap]
rs1113380	0.92[YRI][hapmap]
rs12236896	0.92[YRI][hapmap]
rs12237062	0.92[YRI][hapmap]
rs12346397	0.92[YRI][hapmap]
rs1576958	0.86[ASW][hapmap]
rs16935416	0.92[YRI][hapmap]
rs1759457	0.96[YRI][hapmap]
rs1759464	0.91[YRI][hapmap]
rs1930639	0.92[YRI][hapmap]
rs1930641	0.86[ASW][hapmap];0.92[YRI][hapmap]
rs2151289	0.86[AMR][1000 genomes]
rs2183502	0.81[CEU][hapmap]
rs2210539	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs2483132	0.86[AFR][1000 genomes]
rs2774621	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2774622	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2774623	0.90[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2774626	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2774628	0.86[AFR][1000 genomes]
rs2774629	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2779763	0.86[AMR][1000 genomes]
rs2779766	0.85[AMR][1000 genomes]
rs2779767	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2779768	0.81[CEU][hapmap]
rs2779771	0.89[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2815173	0.80[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2815175	0.92[YRI][hapmap]
rs2815176	0.80[CEU][hapmap]
rs2815177	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2815179	0.86[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap]
rs2815181	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2815182	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2815183	0.81[CEU][hapmap]
rs2815184	0.81[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap]
rs3119847	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3119848	0.95[MEX][hapmap];0.93[TSI][hapmap]
rs3122360	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4128606	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4289910	0.92[YRI][hapmap]
rs4961529	0.86[AMR][1000 genomes]
rs4961534	0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs601960	0.86[ASW][hapmap];0.92[YRI][hapmap]
rs613966	0.86[ASW][hapmap];0.92[YRI][hapmap]
rs620280	0.92[YRI][hapmap]
rs642582	0.92[YRI][hapmap]
rs646025	0.86[ASW][hapmap];0.92[YRI][hapmap]
rs6475109	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6475113	0.81[CEU][hapmap]
rs664447	0.86[ASW][hapmap]
rs7030801	0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs7031361	0.81[YRI][hapmap]
rs7850279	0.86[AMR][1000 genomes]
rs7862706	0.81[CEU][hapmap]
rs7870682	0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs870270	0.86[ASW][hapmap];0.92[YRI][hapmap]
rs9407787	0.86[ASW][hapmap];0.85[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892657	chr9:17008137-17223492	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1023525	chr9:17121773-17236072	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv892659	chr9:17130360-17236376	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv892660	chr9:17134245-17269437	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv428537	chr9:17146369-17308494	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17135800-17154200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:17135800-17155200	Weak transcription	Spleen	Spleen
3	chr9:17136000-17155200	Weak transcription	Fetal Intestine Large	intestine
4	chr9:17136000-17161000	Weak transcription	Psoas Muscle	Psoas
5	chr9:17136200-17148000	Weak transcription	Fetal Kidney	kidney
6	chr9:17136200-17148200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:17136200-17148200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:17136200-17148400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:17136200-17152600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:17136200-17154600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:17136200-17155200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:17136200-17157600	Weak transcription	Fetal Thymus	thymus
13	chr9:17136200-17159200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:17136200-17159600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:17136400-17148000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:17136400-17148000	Weak transcription	Osteobl	bone
17	chr9:17136400-17148200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:17136400-17148400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:17136400-17151800	Weak transcription	NH-A	brain
20	chr9:17136400-17154800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:17136400-17156600	Weak transcription	NHLF	lung
22	chr9:17136400-17159000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:17136400-17163800	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:17136400-17164200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:17136600-17148400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:17136600-17154400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:17136600-17154800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:17136800-17154000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:17136800-17159000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:17137000-17148000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:17137000-17148000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:17137800-17150000	Weak transcription	NHDF-Ad	bronchial
33	chr9:17137800-17160400	Weak transcription	Hela-S3	cervix
34	chr9:17140000-17154000	Weak transcription	Fetal Stomach	stomach
35	chr9:17140800-17147200	Weak transcription	Ovary	ovary
36	chr9:17142800-17154200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr9:17143400-17148800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr9:17143600-17149400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:17143800-17149400	Strong transcription	Liver	Liver
40	chr9:17144200-17155000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:17144400-17154400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr9:17145200-17147200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr9:17145400-17148800	Strong transcription	Dnd41	blood
44	chr9:17145400-17149200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr9:17145600-17147200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:17145600-17149000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:17145800-17148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:17145800-17150000	Weak transcription	HSMM	muscle
49	chr9:17146200-17147200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:17146200-17147400	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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