Variant report

Variant	rs1488
Chromosome Location	chr6:161538250-161538251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161536783..161539702-chr6:161586448..161588143,2	K562	blood:
2	chr6:161535825..161538708-chr6:161688677..161691467,2	K562	blood:
3	chr6:161530149..161531897-chr6:161535661..161538320,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12528950	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs3798917	0.88[CHB][hapmap]
rs4709494	0.82[AFR][1000 genomes]
rs6905734	0.86[YRI][hapmap]
rs9365252	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1488	MAP3K4	cis	thalamus	BrainEAC
rs1488	MAP3K4	cis	inferior olivary nucleus	BrainEAC
rs1488	MAP3K4	cis	parietal	SCAN
rs1488	MAP3K4	cis	occipital cortex	BrainEAC
rs1488	MAP3K4	cis	frontal cortex	BrainEAC
rs1488	MAP3K4	cis	temporal cortex	BrainEAC
rs1488	MAP3K4	cis	cerebellar cortex	BrainEAC
rs1488	MAP3K4	cis	hippocampus	BrainEAC
rs1488	MAP3K4	cis	intralobular white matter	BrainEAC
rs1488	MAP3K4	cis	putamen	BrainEAC
rs1488	MAP3K4	cis	brain	BrainEAC

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161491000-161538400	Strong transcription	Primary B cells from peripheral blood	blood
2	chr6:161491600-161539800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:161494400-161542400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr6:161496000-161539800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:161497800-161539600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:161498000-161541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:161500200-161540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:161500600-161539800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr6:161500600-161541800	Strong transcription	K562	blood
10	chr6:161514000-161544600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:161514400-161539800	Strong transcription	Left Ventricle	heart
12	chr6:161514600-161541000	Strong transcription	Fetal Intestine Large	intestine
13	chr6:161517000-161539600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:161517600-161543000	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:161517800-161540400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:161517800-161542200	Strong transcription	Liver	Liver
17	chr6:161518000-161538600	Strong transcription	Fetal Stomach	stomach
18	chr6:161518000-161539600	Strong transcription	Fetal Muscle Leg	muscle
19	chr6:161518000-161540000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:161518000-161540800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:161518000-161541400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:161518200-161539800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:161521600-161539600	Weak transcription	Hela-S3	cervix
24	chr6:161522400-161542400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr6:161523800-161540800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:161524400-161540000	Strong transcription	HepG2	liver
27	chr6:161525800-161541200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:161526000-161541200	Strong transcription	Dnd41	blood
29	chr6:161526600-161540600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:161526600-161541400	Strong transcription	Placenta	Placenta
31	chr6:161526600-161542200	Strong transcription	Adipose Nuclei	Adipose
32	chr6:161526800-161539600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:161527000-161540000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr6:161527000-161540600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:161527000-161543000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:161527200-161539600	Strong transcription	Fetal Brain Female	brain
37	chr6:161527200-161542800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:161527400-161538400	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr6:161527400-161539600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:161527400-161543600	Strong transcription	Fetal Lung	lung
41	chr6:161527600-161538400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:161527600-161538600	Strong transcription	Brain Germinal Matrix	brain
43	chr6:161527600-161541400	Strong transcription	Brain Hippocampus Middle	brain
44	chr6:161527600-161547800	Weak transcription	Right Atrium	heart
45	chr6:161528200-161538600	Strong transcription	Right Ventricle	heart
46	chr6:161528200-161538800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:161528600-161538800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:161528600-161538800	Strong transcription	HSMM	muscle
49	chr6:161528600-161539800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:161528600-161541000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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