Variant report

Variant	rs6824488
Chromosome Location	chr4:160190115-160190116
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10017696	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11100215	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12499444	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12507095	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13103075	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13145422	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150322	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28562885	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4295222	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6811571	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6816396	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6824247	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6834008	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6835746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6847780	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6848217	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6848706	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7349689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7699824	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9990664	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830129	chr4:160061694-160270760	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1022771	chr4:160188801-160324683	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6824488	GRIA2	cis	cerebellum	SCAN
rs6824488	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160170400-160192800	Weak transcription	Primary T cells from cord blood	blood
3	chr4:160172600-160193000	Weak transcription	Gastric	stomach
4	chr4:160173000-160193200	Weak transcription	Thymus	Thymus
5	chr4:160173200-160192400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:160173400-160192600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:160173400-160194000	Weak transcription	Fetal Intestine Large	intestine
9	chr4:160173400-160194800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:160174000-160203400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:160180200-160192600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:160186000-160196400	Enhancers	Fetal Heart	heart
13	chr4:160186400-160190400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr4:160186800-160225400	Weak transcription	Primary B cells from cord blood	blood
15	chr4:160187400-160190200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr4:160187800-160190200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr4:160188000-160190400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:160188000-160190400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr4:160188000-160191200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:160188200-160190200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:160188200-160190200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:160188200-160190200	Active TSS	Aorta	Aorta
23	chr4:160188200-160191800	Active TSS	Brain Angular Gyrus	brain
24	chr4:160188200-160201800	Weak transcription	Stomach Mucosa	stomach
25	chr4:160188400-160190200	Active TSS	Stomach Smooth Muscle	stomach
26	chr4:160188400-160190400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr4:160188400-160191000	Active TSS	Brain Anterior Caudate	brain
28	chr4:160188400-160191800	Active TSS	Brain Cingulate Gyrus	brain
29	chr4:160188400-160194200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:160188600-160190600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr4:160188600-160190600	Active TSS	Liver	Liver
32	chr4:160188600-160191600	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr4:160188600-160191800	Active TSS	Brain Substantia Nigra	brain
34	chr4:160188600-160192000	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr4:160188600-160193200	Weak transcription	A549	lung
36	chr4:160188800-160190200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr4:160188800-160190400	Active TSS	Brain Germinal Matrix	brain
38	chr4:160188800-160190400	Active TSS	Right Atrium	heart
39	chr4:160188800-160190600	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr4:160188800-160191400	Active TSS	Brain Hippocampus Middle	brain
41	chr4:160188800-160191800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:160188800-160192000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:160188800-160192600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:160188800-160193000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:160188800-160193000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:160188800-160193800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:160188800-160193800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:160188800-160195000	Weak transcription	Lung	lung
49	chr4:160188800-160196000	Weak transcription	Spleen	Spleen
50	chr4:160188800-160205200	Weak transcription	Ovary	ovary

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