Variant report

Variant	rs6896513
Chromosome Location	chr5:179682482-179682483
allele	A/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	chr5:179682424-179682741	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000253908	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1127575	0.93[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs11955223	0.81[AFR][1000 genomes]
rs11960340	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13162206	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17080136	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17627593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33928286	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34428073	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35203283	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4362908	0.93[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs4481314	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs56131100	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61478999	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6601104	0.92[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6703	1.00[CHB][hapmap];0.89[YRI][hapmap]
rs6860142	0.81[AFR][1000 genomes]
rs6874413	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6875134	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7710896	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7724543	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7726664	0.93[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs7730064	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7730091	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs9605	0.92[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6896513	ENSG00000050748	cis	multi-tissue	Pritchard
rs6896513	MAPK9	cis	Lymphoblastoid	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
3	chr5:179656600-179703000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
4	chr5:179657800-179697000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:179660800-179706800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:179665800-179696600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:179666000-179697000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr5:179668200-179696800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
9	chr5:179669400-179683600	Weak transcription	K562	blood
10	chr5:179670200-179712800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:179671200-179694000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
12	chr5:179673600-179691400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:179673600-179694800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr5:179673600-179695200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr5:179673600-179696600	ZNF genes & repeats	Adipose Nuclei	Adipose
16	chr5:179673600-179697000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:179673600-179697000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr5:179673600-179701800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr5:179673600-179705400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:179673800-179696400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:179674200-179684800	ZNF genes & repeats	Fetal Intestine Small	intestine
22	chr5:179674200-179685000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:179674200-179685000	ZNF genes & repeats	Colonic Mucosa	Colon
24	chr5:179674200-179685000	ZNF genes & repeats	Lung	lung
25	chr5:179674200-179685000	ZNF genes & repeats	Spleen	Spleen
26	chr5:179674200-179685200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:179674200-179686000	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr5:179674200-179686200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
29	chr5:179674200-179687000	ZNF genes & repeats	Left Ventricle	heart
30	chr5:179674200-179691400	ZNF genes & repeats	Ovary	ovary
31	chr5:179674200-179691400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
32	chr5:179674200-179696200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:179674200-179696400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:179674200-179696800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr5:179674400-179692800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
36	chr5:179674400-179694800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:179674600-179694000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
38	chr5:179674800-179684800	ZNF genes & repeats	Fetal Stomach	stomach
39	chr5:179674800-179686600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:179674800-179686800	ZNF genes & repeats	Thymus	Thymus
41	chr5:179674800-179696400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr5:179675000-179691400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
43	chr5:179676400-179694800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
44	chr5:179676400-179697400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
45	chr5:179676600-179684800	ZNF genes & repeats	Fetal Thymus	thymus
46	chr5:179676800-179696000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr5:179677000-179687800	ZNF genes & repeats	Fetal Lung	lung
48	chr5:179677000-179696400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
49	chr5:179677000-179703000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:179677400-179686600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin

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