Variant report

Variant	rs1127575
Chromosome Location	chr5:179662384-179662385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179661961..179665660-chr5:179666627..179671316,5	K562	blood:
2	chr5:179660175..179662984-chr5:180235591..180238303,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131446	Chromatin interaction
ENSG00000050748	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11955223	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627593	0.93[CHB][hapmap];0.90[CHD][hapmap];0.84[LWK][hapmap];0.96[YRI][hapmap]
rs4362908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481314	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56131100	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs58528869	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61478999	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6601104	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6703	0.85[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6860142	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896513	0.93[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs7710896	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7724543	0.87[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs7726664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9605	0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1127575	MAPK9	cis	parietal	SCAN
rs1127575	CHP2	trans	cerebellum	SCAN
rs1127575	MAPK9	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179650200-179669000	Weak transcription	Fetal Brain Male	brain
2	chr5:179651600-179678000	Weak transcription	Fetal Heart	heart
3	chr5:179653000-179662800	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:179653600-179662400	Weak transcription	Brain Substantia Nigra	brain
5	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:179655000-179679600	Weak transcription	Stomach Mucosa	stomach
7	chr5:179655200-179663200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
9	chr5:179655800-179666400	ZNF genes & repeats	Aorta	Aorta
10	chr5:179655800-179675400	Strong transcription	Primary B cells from cord blood	blood
11	chr5:179656200-179675000	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr5:179656600-179703000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
13	chr5:179656800-179666000	Weak transcription	NH-A	brain
14	chr5:179657200-179668000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:179657400-179663000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:179657400-179669200	Strong transcription	Fetal Stomach	stomach
17	chr5:179657400-179669200	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:179657400-179673600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:179657400-179674400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:179657600-179667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:179657800-179674400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:179657800-179697000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:179658000-179663200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:179658000-179667600	Weak transcription	NHLF	lung
25	chr5:179658200-179662400	Weak transcription	Psoas Muscle	Psoas
26	chr5:179658200-179663200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr5:179658400-179665800	Strong transcription	Adipose Nuclei	Adipose
28	chr5:179658400-179668200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:179658400-179669600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:179658400-179670600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:179658400-179670800	Strong transcription	Fetal Muscle Leg	muscle
32	chr5:179658400-179672600	Strong transcription	Thymus	Thymus
33	chr5:179658400-179679200	Strong transcription	Primary T cells from cord blood	blood
34	chr5:179658800-179680400	Weak transcription	Fetal Kidney	kidney
35	chr5:179659000-179664800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:179659000-179665200	Strong transcription	Colonic Mucosa	Colon
37	chr5:179659000-179667600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:179659000-179668600	Strong transcription	Ovary	ovary
39	chr5:179659000-179669800	Strong transcription	Placenta	Placenta
40	chr5:179659000-179670800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:179659000-179677600	Strong transcription	Dnd41	blood
42	chr5:179659200-179663600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:179659200-179666000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:179659200-179668800	Weak transcription	K562	blood
45	chr5:179659200-179670000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:179659200-179672600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:179659200-179674200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr5:179659400-179665800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:179659400-179666000	Weak transcription	NHDF-Ad	bronchial
50	chr5:179659400-179674800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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