Variant report

Variant	rs12340503
Chromosome Location	chr9:108501100-108501101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10046878	0.83[AFR][1000 genomes]
rs10113972	0.83[AFR][1000 genomes]
rs10114130	1.00[AFR][1000 genomes]
rs10114801	1.00[AFR][1000 genomes]
rs10115662	0.83[AFR][1000 genomes]
rs10116005	0.96[AFR][1000 genomes]
rs10116197	1.00[AFR][1000 genomes]
rs10120813	0.83[AFR][1000 genomes]
rs10978207	0.83[AFR][1000 genomes]
rs10978217	1.00[AFR][1000 genomes]
rs11506758	0.88[AFR][1000 genomes]
rs11506829	0.96[AFR][1000 genomes]
rs12337252	0.96[AFR][1000 genomes]
rs12342079	0.92[AFR][1000 genomes]
rs12345515	1.00[AFR][1000 genomes]
rs12348005	1.00[AFR][1000 genomes]
rs12348603	0.96[AFR][1000 genomes]
rs12351889	0.86[AFR][1000 genomes]
rs16924936	0.96[AFR][1000 genomes]
rs28877915	0.96[AFR][1000 genomes]
rs57179817	0.96[AFR][1000 genomes]
rs60282712	0.84[AFR][1000 genomes]
rs7025764	0.83[AFR][1000 genomes]
rs7038466	1.00[AFR][1000 genomes]
rs7862382	0.96[AFR][1000 genomes]
rs7863153	0.92[AFR][1000 genomes]
rs7872036	0.96[AFR][1000 genomes]
rs7872193	0.85[AFR][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	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv615116	chr9:108468129-108546438	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108495400-108501400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr9:108495400-108501600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:108497600-108501600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:108497600-108510800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:108498000-108511800	Weak transcription	K562	blood
6	chr9:108498000-108513200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:108498200-108501200	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr9:108498200-108510800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:108498200-108513400	Weak transcription	HSMMtube	muscle
10	chr9:108498400-108520000	Weak transcription	Fetal Heart	heart
11	chr9:108498400-108520400	Weak transcription	Psoas Muscle	Psoas
12	chr9:108498600-108510000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:108498600-108510200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:108498600-108510600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:108498800-108510400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:108498800-108514600	Weak transcription	Small Intestine	intestine
17	chr9:108499000-108510200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:108499000-108510200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr9:108499000-108513400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:108499200-108501200	ZNF genes & repeats	Fetal Intestine Large	intestine
21	chr9:108499200-108510600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:108499200-108515000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:108499400-108510800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr9:108499400-108511600	Weak transcription	Left Ventricle	heart
25	chr9:108499400-108513400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:108499400-108514800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:108499400-108516000	Weak transcription	Brain Anterior Caudate	brain
28	chr9:108499400-108516000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:108499600-108511600	Weak transcription	Pancreas	Pancrea
30	chr9:108499800-108510400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:108499800-108510400	Weak transcription	Liver	Liver
32	chr9:108499800-108513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:108499800-108513400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:108499800-108513400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:108499800-108514800	Weak transcription	Fetal Kidney	kidney
36	chr9:108500000-108502400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr9:108500000-108504400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr9:108500000-108504400	Weak transcription	HepG2	liver
39	chr9:108500000-108511400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:108500000-108511600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:108500000-108513200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:108500000-108513400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:108500000-108513400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr9:108500200-108510800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:108500200-108513400	Weak transcription	Thymus	Thymus
46	chr9:108500400-108501800	Weak transcription	Spleen	Spleen
47	chr9:108500400-108510200	Weak transcription	GM12878-XiMat	blood
48	chr9:108500400-108510400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:108500400-108510400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr9:108500400-108510600	Weak transcription	Fetal Muscle Trunk	muscle

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