Variant report

Variant	rs2416879
Chromosome Location	chr9:102613672-102613673
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:102612792..102615430-chr9:102621366..102623086,2	MCF-7	breast:
2	chr9:102613229..102615330-chr9:102617539..102619648,2	MCF-7	breast:
3	chr9:102605319..102608500-chr9:102612977..102616501,4	K562	blood:

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10819694	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs41274654	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv528025	chr9:102540386-102613672	Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2416879	GABBR2	cis	parietal	SCAN
rs2416879	NANS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102587000-102613800	Weak transcription	Hela-S3	cervix
2	chr9:102591200-102618400	Weak transcription	Brain Angular Gyrus	brain
3	chr9:102591400-102616200	Weak transcription	Lung	lung
4	chr9:102592200-102618400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:102594200-102622000	Weak transcription	Brain Germinal Matrix	brain
6	chr9:102595400-102628200	Weak transcription	Fetal Brain Female	brain
7	chr9:102596200-102616400	Weak transcription	Fetal Brain Male	brain
8	chr9:102596200-102620400	Weak transcription	Fetal Heart	heart
9	chr9:102597200-102621800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:102601400-102620800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:102605400-102621800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:102606800-102615200	Strong transcription	Left Ventricle	heart
13	chr9:102607000-102615400	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:102607000-102617800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:102608600-102614400	Weak transcription	Psoas Muscle	Psoas
16	chr9:102608600-102620400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:102608800-102614000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:102609400-102613800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr9:102609600-102615400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:102609800-102615000	Weak transcription	Ovary	ovary
21	chr9:102609800-102627000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:102610000-102614200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:102610400-102631200	Weak transcription	NHLF	lung
24	chr9:102610400-102644000	Weak transcription	Aorta	Aorta
25	chr9:102610600-102621600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:102610600-102621600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:102611000-102614200	Enhancers	Stomach Mucosa	stomach
28	chr9:102611200-102614000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr9:102611200-102614000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:102611400-102627000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:102611800-102614600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:102611800-102628800	Weak transcription	Right Ventricle	heart
33	chr9:102612000-102615200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr9:102612200-102614200	Enhancers	Small Intestine	intestine
35	chr9:102612200-102615400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:102612200-102618800	Weak transcription	Spleen	Spleen
37	chr9:102612200-102621400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:102612400-102614000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:102612600-102614200	Enhancers	Fetal Stomach	stomach
40	chr9:102612600-102614800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr9:102612600-102615000	Enhancers	Dnd41	blood
42	chr9:102612600-102615200	Enhancers	Primary T cells fromperipheralblood	blood
43	chr9:102612600-102615400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr9:102612800-102614800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:102612800-102614800	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr9:102612800-102615200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:102612800-102615200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:102612800-102628200	Weak transcription	Colon Smooth Muscle	Colon
49	chr9:102613000-102614400	Enhancers	Primary T cells from cord blood	blood
50	chr9:102613000-102614400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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