Variant report

Variant	rs10780598
Chromosome Location	chr9:72349561-72349562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10867952	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10867966	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10867987	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868033	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868041	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11139923	0.82[LWK][hapmap]
rs11139997	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140181	0.92[EUR][1000 genomes]
rs11140185	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140189	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140204	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140205	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140206	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140208	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11791457	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11792104	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11793130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12376529	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13287102	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13293591	1.00[CEU][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13293770	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1411411	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536993	0.86[GIH][hapmap]
rs2026795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56040923	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs918337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1048622	chr9:72303617-72371795	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72323600-72360800	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:72323800-72357600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:72324200-72361000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:72324600-72359800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:72325000-72358800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:72327800-72366800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:72330000-72349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:72330600-72357400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:72333400-72374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:72335200-72350400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:72336000-72352600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:72336600-72359400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:72337200-72350200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:72337400-72366400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:72340200-72349800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:72340200-72350200	Strong transcription	Fetal Lung	lung
17	chr9:72342000-72349600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:72342000-72349600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:72342200-72349600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:72342200-72350200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr9:72342200-72350200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:72342200-72350400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:72342200-72351200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:72342200-72356600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr9:72342200-72356600	Strong transcription	Fetal Thymus	thymus
26	chr9:72342200-72356800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr9:72343000-72350200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:72344200-72349600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:72344200-72349600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr9:72344200-72350200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:72344200-72350600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr9:72344400-72349600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr9:72344400-72350200	Strong transcription	Primary T cells from cord blood	blood
34	chr9:72344600-72349600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr9:72344600-72350200	Strong transcription	Placenta	Placenta
36	chr9:72344600-72350400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr9:72344600-72352000	Strong transcription	Primary B cells from cord blood	blood
38	chr9:72345000-72349800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr9:72345000-72350200	Strong transcription	HSMMtube	muscle
40	chr9:72345000-72350400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr9:72345200-72349800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr9:72345400-72359000	Weak transcription	Pancreas	Pancrea
43	chr9:72345600-72349600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:72346000-72349600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr9:72346600-72360000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:72347000-72353000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:72347000-72364600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr9:72347200-72358800	Weak transcription	Fetal Heart	heart
49	chr9:72347200-72360600	Weak transcription	Brain Substantia Nigra	brain
50	chr9:72347200-72361600	Weak transcription	Ovary	ovary

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