Variant report

Variant	rs2154079
Chromosome Location	chr9:95956291-95956292
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10821083	0.80[CEU][hapmap];0.80[TSI][hapmap]
rs10821087	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992671	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11790340	0.96[YRI][hapmap]
rs12000524	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv614880	chr9:95930572-95978265	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2154079	NCRNA00242	trans	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95948200-95958400	Weak transcription	Lung	lung
2	chr9:95950000-95960800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:95950800-95967400	Enhancers	Fetal Heart	heart
4	chr9:95953400-95957600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr9:95953800-95956800	Enhancers	Right Ventricle	heart
6	chr9:95954400-95956400	Enhancers	Pancreas	Pancrea
7	chr9:95954400-95957200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr9:95954400-95957400	Enhancers	Fetal Brain Male	brain
9	chr9:95954600-95957000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr9:95954600-95957200	Enhancers	Brain Cingulate Gyrus	brain
11	chr9:95954600-95957200	Enhancers	Colon Smooth Muscle	Colon
12	chr9:95954600-95957200	Enhancers	Fetal Muscle Leg	muscle
13	chr9:95954600-95957200	Enhancers	Rectal Smooth Muscle	rectum
14	chr9:95954600-95961600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr9:95954800-95956800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:95954800-95957400	Enhancers	Fetal Brain Female	brain
17	chr9:95954800-95959600	Enhancers	Duodenum Mucosa	Duodenum
18	chr9:95955000-95956600	Enhancers	Fetal Intestine Large	intestine
19	chr9:95955000-95957400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr9:95955200-95957000	Enhancers	H9 Cell Line	embryonic stem cell
21	chr9:95955200-95957000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr9:95955200-95957200	Enhancers	Stomach Mucosa	stomach
23	chr9:95955400-95956400	Enhancers	Fetal Intestine Small	intestine
24	chr9:95955400-95956800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:95955400-95957400	Enhancers	Fetal Lung	lung
26	chr9:95955400-95959000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:95955600-95956800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:95955600-95957000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:95955600-95957200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr9:95955600-95957200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr9:95955600-95957200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:95955600-95957400	Enhancers	Stomach Smooth Muscle	stomach
33	chr9:95955600-95958200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:95955600-95961600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr9:95955800-95956600	Weak transcription	HepG2	liver
36	chr9:95955800-95957000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr9:95955800-95957200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr9:95955800-95957200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr9:95955800-95957200	Enhancers	Fetal Stomach	stomach
40	chr9:95955800-95959000	Weak transcription	Right Atrium	heart
41	chr9:95955800-95960200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr9:95955800-95985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:95956000-95956400	Weak transcription	Brain Angular Gyrus	brain
44	chr9:95956000-95956400	Weak transcription	Brain Anterior Caudate	brain
45	chr9:95956000-95956400	Weak transcription	Esophagus	oesophagus
46	chr9:95956000-95957200	Enhancers	Brain Germinal Matrix	brain
47	chr9:95956000-95958200	Weak transcription	Left Ventricle	heart
48	chr9:95956000-95959000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:95956000-95959000	Weak transcription	Colonic Mucosa	Colon
50	chr9:95956000-95960000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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