Variant report

Variant	rs6601104
Chromosome Location	chr5:179663614-179663615
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:

Variant related genes	Relation type
ENSG00000050748	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1127575	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]
rs11955223	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11960340	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13162206	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17080136	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17627593	0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs33928286	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34428073	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35203283	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4362908	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4481314	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs56131100	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58528869	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs61478999	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6703	0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.95[ASN][1000 genomes]
rs6860142	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6874413	0.92[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6875134	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6896513	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]
rs7710896	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724543	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7726664	0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7730064	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7730091	0.88[CEU][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9605	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6601104	RASGEF1C	cis	parietal	SCAN
rs6601104	FAM26E	trans	cerebellum	SCAN
rs6601104	FLT4	cis	cerebellum	SCAN
rs6601104	MAPK9	cis	lymphoblastoid	seeQTL
rs6601104	MAPK9	cis	Lymphoblastoid	GTEx
rs6601104	MAPK9	cis	parietal	SCAN
rs6601104	MAPK9	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:179655000-179679600	Weak transcription	Stomach Mucosa	stomach
5	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
6	chr5:179655800-179666400	ZNF genes & repeats	Aorta	Aorta
7	chr5:179655800-179675400	Strong transcription	Primary B cells from cord blood	blood
8	chr5:179656200-179675000	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:179656600-179703000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
10	chr5:179656800-179666000	Weak transcription	NH-A	brain
11	chr5:179657200-179668000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:179657400-179669200	Strong transcription	Fetal Stomach	stomach
13	chr5:179657400-179669200	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:179657400-179673600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:179657400-179674400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:179657600-179667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:179657800-179674400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:179657800-179697000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:179658000-179667600	Weak transcription	NHLF	lung
20	chr5:179658400-179665800	Strong transcription	Adipose Nuclei	Adipose
21	chr5:179658400-179668200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:179658400-179669600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:179658400-179670600	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:179658400-179670800	Strong transcription	Fetal Muscle Leg	muscle
25	chr5:179658400-179672600	Strong transcription	Thymus	Thymus
26	chr5:179658400-179679200	Strong transcription	Primary T cells from cord blood	blood
27	chr5:179658800-179680400	Weak transcription	Fetal Kidney	kidney
28	chr5:179659000-179664800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:179659000-179665200	Strong transcription	Colonic Mucosa	Colon
30	chr5:179659000-179667600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:179659000-179668600	Strong transcription	Ovary	ovary
32	chr5:179659000-179669800	Strong transcription	Placenta	Placenta
33	chr5:179659000-179670800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:179659000-179677600	Strong transcription	Dnd41	blood
35	chr5:179659200-179666000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr5:179659200-179668800	Weak transcription	K562	blood
37	chr5:179659200-179670000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:179659200-179672600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:179659200-179674200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr5:179659400-179665800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:179659400-179666000	Weak transcription	NHDF-Ad	bronchial
42	chr5:179659400-179674800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:179659600-179674200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:179659800-179665000	Strong transcription	Brain Angular Gyrus	brain
45	chr5:179659800-179667800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:179660000-179664800	Strong transcription	A549	lung
47	chr5:179660000-179669600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr5:179660000-179670800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr5:179660200-179664800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:179660200-179668200	Strong transcription	Primary neutrophils fromperipheralblood	blood

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