Variant report

Variant	rs6816396
Chromosome Location	chr4:160239445-160239446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10017696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10021753	0.82[YRI][hapmap]
rs11100215	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11723634	0.80[GIH][hapmap];1.00[YRI][hapmap]
rs12499444	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12507095	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13103075	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13145422	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];0.85[EUR][1000 genomes]
rs13147632	1.00[YRI][hapmap]
rs13150322	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28562885	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749465	0.85[YRI][hapmap]
rs4295222	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6811571	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6824247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824488	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]
rs6834008	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6835746	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6847780	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6848217	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6848706	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7349689	0.96[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7699824	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9990664	0.96[AMR][1000 genomes];0.89[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6816396	GRIA2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160193400-160240200	Weak transcription	Gastric	stomach
2	chr4:160205800-160260600	Weak transcription	Aorta	Aorta
3	chr4:160217000-160259400	Weak transcription	Fetal Brain Male	brain
4	chr4:160220000-160244400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:160223000-160260000	Weak transcription	Ovary	ovary
6	chr4:160224600-160262400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:160225200-160260200	Weak transcription	Thymus	Thymus
8	chr4:160225600-160253600	Weak transcription	HepG2	liver
9	chr4:160226000-160260800	Weak transcription	Colonic Mucosa	Colon
10	chr4:160226200-160244000	Weak transcription	Fetal Kidney	kidney
11	chr4:160226200-160270600	Weak transcription	Small Intestine	intestine
12	chr4:160226400-160242400	Weak transcription	GM12878-XiMat	blood
13	chr4:160229000-160242600	Weak transcription	Right Atrium	heart
14	chr4:160229200-160247600	Weak transcription	Stomach Mucosa	stomach
15	chr4:160230000-160251800	Weak transcription	NHDF-Ad	bronchial
16	chr4:160230200-160263800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:160230200-160270800	Weak transcription	A549	lung
18	chr4:160230400-160243400	Weak transcription	NH-A	brain
19	chr4:160230400-160244000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:160230400-160253600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:160230400-160259400	Weak transcription	NHLF	lung
22	chr4:160230400-160260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:160230400-160260600	Weak transcription	HSMMtube	muscle
24	chr4:160230600-160260000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:160231000-160240000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:160231000-160243400	Weak transcription	NHEK	skin
27	chr4:160231000-160243600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:160231000-160244000	Weak transcription	HUVEC	blood vessel
29	chr4:160231000-160259400	Weak transcription	HMEC	breast
30	chr4:160231000-160260400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:160231000-160260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:160232200-160274600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:160232800-160240200	Weak transcription	Right Ventricle	heart
34	chr4:160232800-160253400	Weak transcription	Psoas Muscle	Psoas
35	chr4:160233000-160244200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr4:160233000-160253400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:160233000-160260000	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:160233600-160243600	Weak transcription	Dnd41	blood
39	chr4:160233600-160244000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:160233600-160259600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:160233800-160242600	Weak transcription	Fetal Heart	heart
42	chr4:160233800-160264000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:160234000-160259400	Weak transcription	Esophagus	oesophagus
44	chr4:160234200-160260200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:160235000-160248200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr4:160235200-160243400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr4:160235200-160248200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr4:160235200-160266200	Weak transcription	Spleen	Spleen
49	chr4:160236000-160243400	Weak transcription	Primary B cells from cord blood	blood
50	chr4:160236000-160252600	Weak transcription	Osteobl	bone

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