Variant report

Variant	rs2768290
Chromosome Location	chr9:108322117-108322118
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10115299	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10761100	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816278	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10820809	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10820810	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10820812	0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10820813	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1327354	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1360089	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1806898	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1815383	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1960023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1987634	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2225246	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2427769	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2518106	0.96[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2518112	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518114	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518116	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2518120	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2518123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2518124	0.93[ASN][1000 genomes]
rs2518128	0.96[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2518131	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2768279	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2768280	0.93[EUR][1000 genomes]
rs2768283	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2768291	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2768292	0.93[ASN][1000 genomes]
rs2768294	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2771038	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2771041	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2771042	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2812297	0.84[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs2812303	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2812307	0.91[ASN][1000 genomes]
rs2812308	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2812310	0.94[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs4742650	0.84[ASN][1000 genomes]
rs4742947	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4742948	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6477447	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6477449	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7020083	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7357632	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7864020	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049133	chr9:108292302-108356068	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321000-108324400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:108321000-108324400	Weak transcription	Esophagus	oesophagus
3	chr9:108321200-108322200	Enhancers	Primary hematopoietic stem cells	blood
4	chr9:108321200-108323000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:108321200-108323200	Weak transcription	Ovary	ovary
6	chr9:108321200-108325600	Weak transcription	Left Ventricle	heart
7	chr9:108321200-108335600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:108321400-108322200	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr9:108321400-108323000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:108321400-108323000	Weak transcription	Fetal Intestine Small	intestine
11	chr9:108321400-108323400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:108321400-108323800	Weak transcription	Fetal Heart	heart
13	chr9:108321400-108324000	Weak transcription	Primary B cells from cord blood	blood
14	chr9:108321400-108324400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:108321400-108324600	Weak transcription	Fetal Kidney	kidney
16	chr9:108321400-108325000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:108321600-108322200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:108321600-108322200	Active TSS	GM12878-XiMat	blood
19	chr9:108321600-108322200	Enhancers	HepG2	liver
20	chr9:108321600-108322800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:108321600-108323000	Weak transcription	Fetal Stomach	stomach
22	chr9:108321600-108323400	Weak transcription	Primary T cells from cord blood	blood
23	chr9:108321600-108323400	Weak transcription	Liver	Liver
24	chr9:108321600-108323800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:108321600-108323800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:108321600-108323800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:108321600-108323800	Weak transcription	Fetal Lung	lung
28	chr9:108321600-108324000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:108321600-108324000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:108321600-108324000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:108321600-108324200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:108321600-108324200	Weak transcription	A549	lung
33	chr9:108321600-108324400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:108321600-108324400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr9:108321600-108324400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:108321600-108324400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:108321600-108324400	Weak transcription	Fetal Brain Male	brain
38	chr9:108321600-108324400	Weak transcription	NHEK	skin
39	chr9:108321600-108324400	Weak transcription	NHLF	lung
40	chr9:108321600-108325000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:108321600-108325000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr9:108321600-108325200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr9:108321600-108325600	Weak transcription	Thymus	Thymus
44	chr9:108321600-108326000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr9:108321600-108326200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:108321600-108336000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:108321600-108336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:108321600-108336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr9:108321600-108338000	Weak transcription	Colon Smooth Muscle	Colon
50	chr9:108321600-108353600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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