Variant report

Variant	rs12552534
Chromosome Location	chr9:116870740-116870741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116869935..116870873-chr9:117052125..117052932,3	K562	blood:
2	chr9:116869905..116870808-chr9:117026020..117026989,3	MCF-7	breast:
3	chr9:116869916..116870857-chr9:117067860..117068426,2	K562	blood:
4	chr9:116870303..116871233-chr9:117051501..117052146,3	MCF-7	breast:
5	chr9:116870044..116870759-chr9:117033677..117034476,3	MCF-7	breast:
6	chr9:116869961..116870829-chr9:117067901..117068666,2	MCF-7	breast:
7	chr9:116870168..116870856-chr9:116901035..116901659,2	MCF-7	breast:
8	chr9:116869895..116870973-chr9:117052879..117053661,10	MCF-7	breast:
9	chr9:116869949..116870838-chr9:116915614..116916621,9	MCF-7	breast:
10	chr9:116869902..116871221-chr9:117033694..117034751,11	MCF-7	breast:
11	chr9:116869078..116871087-chr9:117033811..117035957,3	MCF-7	breast:
12	chr9:116869891..116870803-chr9:116915238..116916605,3	MCF-7	breast:
13	chr9:116856264..116859004-chr9:116870407..116871935,2	MCF-7	breast:
14	chr9:116864243..116866474-chr9:116868618..116871598,3	MCF-7	breast:
15	chr9:116869941..116870862-chr9:117026162..117027038,2	K562	blood:
16	chr9:116869934..116871127-chr9:117052704..117054035,13	MCF-7	breast:
17	chr9:116869923..116871115-chr9:117053002..117053726,3	K562	blood:
18	chr9:116870237..116871907-chr9:116924776..116927376,2	MCF-7	breast:
19	chr9:116870116..116870941-chr9:116916806..116918287,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196739	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

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	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
5	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
6	nsv893751	chr9:116846467-116874355	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12552534	TNFSF15	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116865600-116870800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:116868000-116871400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:116869800-116870800	Enhancers	Fetal Lung	lung
4	chr9:116870000-116870800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:116870000-116870800	Enhancers	Placenta	Placenta
6	chr9:116870000-116870800	Enhancers	Stomach Mucosa	stomach
7	chr9:116870000-116871000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:116870000-116871000	Enhancers	Brain Hippocampus Middle	brain
9	chr9:116870000-116871000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr9:116870000-116871200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:116870000-116871200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr9:116870000-116871400	Enhancers	Brain Substantia Nigra	brain
13	chr9:116870000-116871600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:116870000-116871600	Flanking Active TSS	HepG2	liver
15	chr9:116870000-116873400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:116870000-116873400	Enhancers	A549	lung
17	chr9:116870200-116870800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:116870200-116870800	Enhancers	Fetal Intestine Large	intestine
19	chr9:116870200-116871000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:116870200-116871600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:116870200-116871800	Enhancers	Fetal Muscle Leg	muscle
22	chr9:116870400-116870800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:116870400-116871200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:116870400-116871600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr9:116870400-116874800	Weak transcription	Right Atrium	heart
26	chr9:116870600-116871000	Enhancers	Fetal Thymus	thymus
27	chr9:116870600-116871200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:116870600-116871200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:116870600-116871200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr9:116870600-116871200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr9:116870600-116871400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
32	chr9:116870600-116871400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:116870600-116871600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:116870600-116871600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
35	chr9:116870600-116872200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:116870600-116872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:116870600-116875400	Weak transcription	Right Ventricle	heart

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