Variant report

Variant	rs12342079
Chromosome Location	chr9:108497164-108497165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10046878	1.00[YRI][hapmap]
rs10114130	0.92[AFR][1000 genomes]
rs10114801	0.92[AFR][1000 genomes]
rs10116005	0.89[AFR][1000 genomes]
rs10116197	0.92[AFR][1000 genomes]
rs10120813	1.00[YRI][hapmap]
rs10978217	0.92[AFR][1000 genomes]
rs11506758	0.82[AFR][1000 genomes]
rs11506829	0.89[AFR][1000 genomes]
rs12337252	0.89[AFR][1000 genomes]
rs12338387	1.00[YRI][hapmap]
rs12340503	0.92[AFR][1000 genomes]
rs12345515	0.85[YRI][hapmap];0.92[AFR][1000 genomes]
rs12348005	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12348603	0.89[AFR][1000 genomes]
rs16924936	0.89[AFR][1000 genomes]
rs16924946	0.85[YRI][hapmap]
rs28877915	0.89[AFR][1000 genomes]
rs57179817	0.89[AFR][1000 genomes]
rs7038466	0.92[AFR][1000 genomes]
rs7862382	0.89[AFR][1000 genomes]
rs7863153	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7872036	0.89[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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108458000-108497800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr9:108473200-108497200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr9:108473200-108499800	Weak transcription	Gastric	stomach
4	chr9:108476200-108497800	Weak transcription	Psoas Muscle	Psoas
5	chr9:108476400-108498200	Weak transcription	Left Ventricle	heart
6	chr9:108481600-108497600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:108484200-108497200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:108484800-108497600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:108488000-108497200	Weak transcription	K562	blood
10	chr9:108494000-108497600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:108494000-108498000	Weak transcription	Ovary	ovary
12	chr9:108495000-108497400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:108495400-108499400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
14	chr9:108495400-108500000	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr9:108495400-108500000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr9:108495400-108501400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:108495400-108501600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:108495600-108499000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr9:108496000-108498600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr9:108496400-108497600	Strong transcription	Primary hematopoietic stem cells	blood
21	chr9:108496400-108498400	ZNF genes & repeats	Primary T cells from cord blood	blood
22	chr9:108496400-108499200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:108496400-108500800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:108496600-108500400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:108497000-108497400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
26	chr9:108497000-108497800	ZNF genes & repeats	Liver	Liver
27	chr9:108497000-108498000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:108497000-108499400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr9:108497000-108500000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr9:108497000-108500000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
31	chr9:108497000-108500400	ZNF genes & repeats	Brain Hippocampus Middle	brain

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