Variant report

Variant	rs12520876
Chromosome Location	chr5:179722533-179722534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179722312-179723327	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:179722440-179722874	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:179722314-179723360	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr5:179722526-179723353	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:179722368-179722940	Raji	blood:	n/a	n/a
6	POLR2A	chr5:179722322-179722609	K562	blood:	n/a	n/a
7	POLR2A	chr5:179721307-179723019	SK-N-MC	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179720972..179723069-chr5:179918796..179921248,2	MCF-7	breast:
2	chr5:179720624..179723530-chr5:179725711..179728473,2	K562	blood:
3	chr5:179715674..179717304-chr5:179721521..179723626,2	K562	blood:
4	chr5:179721389..179723686-chr5:179731790..179733996,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNOT6-4	chr5:179719184-179722539	NONHSAT105673

No data

Variant related genes	Relation type
MAPK9	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1363516	0.86[LWK][hapmap]
rs4700933	0.86[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
8	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv10787	chr5:179717724-179732388	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12520876	MAPK9	cis	lymphoblastoid	seeQTL
rs12520876	SAMD9	trans	parietal	SCAN
rs12520876	MAPK9	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720000-179722800	Weak transcription	HSMMtube	muscle
2	chr5:179720000-179727400	Weak transcription	Ovary	ovary
3	chr5:179720600-179722600	Enhancers	Primary hematopoietic stem cells	blood
4	chr5:179720600-179722600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:179720600-179722600	Weak transcription	Brain Germinal Matrix	brain
6	chr5:179720600-179722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:179720600-179722800	Weak transcription	Colonic Mucosa	Colon
8	chr5:179720600-179723000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:179720600-179723200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:179720600-179723200	Weak transcription	Fetal Intestine Large	intestine
11	chr5:179720600-179724800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:179720600-179725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:179720600-179726800	Weak transcription	Osteobl	bone
14	chr5:179720600-179727200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:179720600-179727200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:179720600-179727200	Weak transcription	HSMM	muscle
17	chr5:179720600-179727400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:179720600-179727400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:179720600-179727400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:179720600-179727600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:179720600-179727600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:179720600-179727600	Weak transcription	NH-A	brain
23	chr5:179720600-179727800	Weak transcription	Aorta	Aorta
24	chr5:179720600-179727800	Weak transcription	Lung	lung
25	chr5:179720600-179728200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:179720600-179729600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:179720600-179730400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:179720600-179731400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:179720600-179739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:179720600-179742800	Weak transcription	Right Ventricle	heart
31	chr5:179720600-179743200	Weak transcription	Fetal Lung	lung
32	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
33	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:179720800-179722800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:179720800-179724200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:179720800-179727400	Weak transcription	Fetal Brain Female	brain
37	chr5:179720800-179727800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:179720800-179728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:179720800-179730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:179720800-179743600	Weak transcription	Right Atrium	heart
41	chr5:179720800-179747000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:179721000-179722600	Weak transcription	Pancreas	Pancrea
43	chr5:179721000-179723600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:179721000-179723600	Weak transcription	HepG2	liver
45	chr5:179721000-179724600	Weak transcription	Hela-S3	cervix
46	chr5:179721000-179726800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:179721000-179727000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:179721000-179727000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:179721000-179727200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:179721000-179727400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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