Variant report

Variant	rs17627880
Chromosome Location	chr5:179694178-179694179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179692323..179695194-chr5:179741562..179744368,2	K562	blood:
2	chr5:179692679..179694795-chr5:179697303..179699548,2	K562	blood:
3	chr5:179693858..179696723-chr5:179696767..179698335,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1127580	0.81[EUR][1000 genomes]
rs17627536	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17627815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17629575	1.00[CHB][hapmap]
rs34763496	0.81[EUR][1000 genomes]
rs35067749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35211991	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35394934	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35551113	0.90[AMR][1000 genomes]
rs35759987	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4441844	0.94[CEU][hapmap]
rs4454029	0.95[CEU][hapmap]
rs4469167	0.90[CEU][hapmap]
rs55756747	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62406979	0.86[ASN][1000 genomes]
rs62406981	0.86[ASN][1000 genomes]
rs62406982	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62406984	0.84[EUR][1000 genomes]
rs62406991	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6869231	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6877489	0.81[CEU][hapmap]
rs6882940	0.95[CEU][hapmap]
rs6893005	0.82[AMR][1000 genomes]
rs6894217	0.85[EUR][1000 genomes]
rs7708873	0.80[CEU][hapmap]
rs7722861	0.80[CEU][hapmap]

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
rs17627880	RASGEF1C	cis	parietal	SCAN
rs17627880	MAPK9	cis	lymphoblastoid	seeQTL
rs17627880	MAPK9	cis	multi-tissue	Pritchard
rs17627880	MAPK9	Cis_1M	lymphoblastoid	RTeQTL
rs17627880	BTNL3	cis	parietal	SCAN
rs17627880	MAPK9	cis	cerebellum	SCAN

Chromatin state (count:119 , 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	chr5:179670200-179712800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:179673600-179694800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr5:179673600-179695200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr5:179673600-179696600	ZNF genes & repeats	Adipose Nuclei	Adipose
13	chr5:179673600-179697000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:179673600-179697000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr5:179673600-179701800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr5:179673600-179705400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:179673800-179696400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:179674200-179696200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:179674200-179696400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:179674200-179696800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
21	chr5:179674400-179694800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:179674800-179696400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
23	chr5:179676400-179694800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
24	chr5:179676400-179697400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
25	chr5:179676800-179696000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
26	chr5:179677000-179696400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
27	chr5:179677000-179703000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:179678200-179694200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr5:179678200-179696800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr5:179679000-179694200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
31	chr5:179679200-179694200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
32	chr5:179679200-179694800	ZNF genes & repeats	Dnd41	blood
33	chr5:179679200-179696600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:179679400-179697400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
35	chr5:179679800-179694200	ZNF genes & repeats	Brain Anterior Caudate	brain
36	chr5:179680000-179694200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
37	chr5:179680000-179694200	ZNF genes & repeats	Brain Hippocampus Middle	brain
38	chr5:179681800-179705600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:179682000-179694800	ZNF genes & repeats	Primary T cells from cord blood	blood
40	chr5:179682200-179694200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
41	chr5:179683000-179695200	ZNF genes & repeats	Psoas Muscle	Psoas
42	chr5:179683400-179694200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
43	chr5:179683400-179694800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
44	chr5:179683600-179694200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
45	chr5:179683600-179695600	ZNF genes & repeats	A549	lung
46	chr5:179684000-179694800	ZNF genes & repeats	GM12878-XiMat	blood
47	chr5:179685000-179696400	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr5:179686200-179694200	ZNF genes & repeats	Colonic Mucosa	Colon
49	chr5:179686400-179694200	ZNF genes & repeats	Colon Smooth Muscle	Colon
50	chr5:179687400-179696400	ZNF genes & repeats	Fetal Intestine Large	intestine

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