Variant report

Variant	rs6877489
Chromosome Location	chr5:179677545-179677546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179647507..179649585-chr5:179676137..179678589,2	K562	blood:
2	chr5:179675041..179677707-chr5:179682161..179684985,2	K562	blood:
3	chr5:179668812..179671072-chr5:179675335..179678649,3	MCF-7	breast:
4	chr5:179670436..179673688-chr5:179675507..179679295,5	K562	blood:

Variant related genes	Relation type
ENSG00000050748	Chromatin interaction
ENSG00000253908	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1559113	0.82[ASW][hapmap]
rs17627536	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17627880	0.81[CEU][hapmap]
rs2892152	0.82[ASW][hapmap]
rs3099063	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs35394934	0.84[EUR][1000 genomes]
rs35759987	0.84[EUR][1000 genomes]
rs4441844	0.84[CEU][hapmap]
rs4454029	0.86[CEU][hapmap]
rs4469167	0.80[CEU][hapmap]
rs55756747	0.84[EUR][1000 genomes]
rs62406991	0.83[EUR][1000 genomes]
rs6882940	0.86[CEU][hapmap]
rs6894217	0.83[EUR][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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6877489	FLT4	cis	cerebellum	SCAN
rs6877489	MAPK9	cis	cerebellum	SCAN
rs6877489	RASGEF1C	cis	parietal	SCAN
rs6877489	MAPK9	cis	lymphoblastoid	seeQTL
rs6877489	MAPK9	Cis_1M	lymphoblastoid	RTeQTL
rs6877489	CANX	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179651600-179678000	Weak transcription	Fetal Heart	heart
2	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:179655000-179679600	Weak transcription	Stomach Mucosa	stomach
4	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
5	chr5:179656600-179703000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
6	chr5:179657800-179697000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:179658400-179679200	Strong transcription	Primary T cells from cord blood	blood
8	chr5:179658800-179680400	Weak transcription	Fetal Kidney	kidney
9	chr5:179659000-179677600	Strong transcription	Dnd41	blood
10	chr5:179660200-179679800	Weak transcription	HUVEC	blood vessel
11	chr5:179660400-179677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:179660800-179706800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:179665800-179696600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:179666000-179697000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr5:179668000-179678400	Weak transcription	Brain Substantia Nigra	brain
16	chr5:179668200-179696800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
17	chr5:179669400-179683600	Weak transcription	K562	blood
18	chr5:179669800-179678200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr5:179670200-179681600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:179670200-179712800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:179671200-179694000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
22	chr5:179672600-179677600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr5:179673600-179677600	Strong transcription	Brain Anterior Caudate	brain
24	chr5:179673600-179677600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
25	chr5:179673600-179677800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:179673600-179678400	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr5:179673600-179691400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:179673600-179694800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr5:179673600-179695200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr5:179673600-179696600	ZNF genes & repeats	Adipose Nuclei	Adipose
31	chr5:179673600-179697000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:179673600-179697000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
33	chr5:179673600-179701800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr5:179673600-179705400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:179673800-179677600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:179673800-179696400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:179674000-179678400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:179674200-179677600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr5:179674200-179677600	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr5:179674200-179677600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr5:179674200-179677600	Strong transcription	HepG2	liver
42	chr5:179674200-179677800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr5:179674200-179677800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
44	chr5:179674200-179677800	ZNF genes & repeats	Pancreas	Pancrea
45	chr5:179674200-179677800	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr5:179674200-179678400	Strong transcription	Fetal Muscle Leg	muscle
47	chr5:179674200-179679800	ZNF genes & repeats	GM12878-XiMat	blood
48	chr5:179674200-179680800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:179674200-179680800	ZNF genes & repeats	Aorta	Aorta
50	chr5:179674200-179680800	ZNF genes & repeats	Esophagus	oesophagus

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