Variant report

Variant	rs2899642
Chromosome Location	chr15:59323048-59323049
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59322868-59324036	K562	blood:	n/a	n/a

Variant related genes	Relation type
RNF111	TF binding region

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11636707	0.89[CEU][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11855063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4774319	0.89[JPT][hapmap];0.82[AFR][1000 genomes]
rs72745097	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
3	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv904271	chr15:59249584-59393011	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv520679	chr15:59268410-59376531	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv520872	chr15:59268410-59395184	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv510663	chr15:59310676-59370041	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2899642	RNF111	cis	cerebellar cortex	BrainEAC

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59280800-59327800	Weak transcription	Small Intestine	intestine
2	chr15:59281200-59352600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:59281400-59323200	Weak transcription	Ovary	ovary
4	chr15:59281400-59347800	Weak transcription	Colonic Mucosa	Colon
5	chr15:59281800-59352200	Weak transcription	Aorta	Aorta
6	chr15:59281800-59353400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:59282000-59323200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:59282000-59323200	Weak transcription	Fetal Kidney	kidney
9	chr15:59282400-59323200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:59282400-59323400	Weak transcription	NHLF	lung
11	chr15:59283800-59329000	Weak transcription	Pancreas	Pancrea
12	chr15:59283800-59344800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:59283800-59359000	Weak transcription	Fetal Brain Male	brain
14	chr15:59285000-59328000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:59288400-59351200	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:59295200-59349200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:59295600-59335400	Weak transcription	Lung	lung
18	chr15:59295800-59323200	Weak transcription	Thymus	Thymus
19	chr15:59297800-59323200	Weak transcription	HepG2	liver
20	chr15:59297800-59323200	Weak transcription	NH-A	brain
21	chr15:59298600-59323200	Weak transcription	Adipose Nuclei	Adipose
22	chr15:59298800-59323200	Weak transcription	HMEC	breast
23	chr15:59300000-59324600	Weak transcription	Right Ventricle	heart
24	chr15:59301200-59335400	Weak transcription	HUVEC	blood vessel
25	chr15:59303800-59323200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:59305400-59354400	Weak transcription	Gastric	stomach
27	chr15:59306000-59353400	Weak transcription	Fetal Heart	heart
28	chr15:59306600-59323200	Weak transcription	HSMMtube	muscle
29	chr15:59306800-59323200	Weak transcription	Brain Angular Gyrus	brain
30	chr15:59306800-59323400	Weak transcription	Brain Anterior Caudate	brain
31	chr15:59307200-59323400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:59308400-59358000	Weak transcription	Spleen	Spleen
33	chr15:59309000-59323200	Weak transcription	Fetal Brain Female	brain
34	chr15:59309200-59323200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:59309200-59323400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:59309200-59336600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:59309200-59359000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:59309400-59323200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:59309400-59323200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:59309600-59323200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:59310600-59323200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:59311800-59323200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:59313000-59323200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:59313000-59323200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:59313600-59328600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:59315200-59323200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:59315200-59323200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:59315200-59323200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr15:59315200-59325000	Weak transcription	HSMM	muscle
50	chr15:59317400-59323200	Weak transcription	Primary T cells fromperipheralblood	blood

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