Variant report

Variant	rs6811571
Chromosome Location	chr4:160202107-160202108
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr4:160201441-160202132	HepG2	liver:	n/a	n/a
2	EP300	chr4:160201353-160202112	A549	lung:	n/a	n/a
3	STAT3	chr4:160202088-160202139	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA1	chr4:160201433-160202201	HepG2	liver:	n/a	n/a
5	EP300	chr4:160201608-160202109	HepG2	liver:	n/a	n/a
6	ARID3A	chr4:160201483-160202136	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:24968576..24969555-chr4:160202021..160202538,3	Hela-S3	cervix:
2	chr4:160195585..160197121-chr4:160200675..160203435,2	K562	blood:

Variant related genes	Relation type
RAPGEF2	TF binding region
ENSG00000133226	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10017696	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10022399	0.80[GIH][hapmap]
rs11100215	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11723634	0.83[GIH][hapmap]
rs12499444	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12507095	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13103075	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13145422	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13150322	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28562885	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4295222	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6816396	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];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6824488	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]
rs6834008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835746	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6847780	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6848217	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6848706	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7349689	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9990664	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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
rs6811571	GRIA2	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:160174000-160203400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:160186800-160225400	Weak transcription	Primary B cells from cord blood	blood
5	chr4:160188800-160205200	Weak transcription	Ovary	ovary
6	chr4:160189400-160203000	Weak transcription	Psoas Muscle	Psoas
7	chr4:160189400-160235200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:160190200-160205000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:160190400-160203600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:160190600-160203000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:160190600-160205000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:160191200-160203000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:160193400-160205600	Weak transcription	Right Ventricle	heart
14	chr4:160193400-160240200	Weak transcription	Gastric	stomach
15	chr4:160194200-160210000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:160194400-160202800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:160194400-160203000	Weak transcription	HSMMtube	muscle
18	chr4:160194400-160209600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:160194400-160235600	Weak transcription	Fetal Stomach	stomach
20	chr4:160194400-160236600	Weak transcription	Primary T cells from cord blood	blood
21	chr4:160194600-160203000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:160194600-160203200	Weak transcription	Fetal Brain Female	brain
23	chr4:160194600-160203600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:160194600-160205000	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:160194600-160209400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:160194800-160203000	Weak transcription	Hela-S3	cervix
27	chr4:160194800-160203600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:160195200-160203600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:160195200-160203600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:160195200-160209800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:160195200-160225600	Weak transcription	Placenta	Placenta
32	chr4:160195400-160203000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:160195400-160205200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:160196200-160203000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:160196200-160203000	Weak transcription	NHDF-Ad	bronchial
36	chr4:160196200-160203600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:160196200-160205000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:160196400-160203000	Weak transcription	HSMM	muscle
39	chr4:160196400-160203200	Weak transcription	Fetal Brain Male	brain
40	chr4:160196400-160203600	Weak transcription	Fetal Lung	lung
41	chr4:160196800-160202800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:160197400-160203800	Weak transcription	HUVEC	blood vessel
43	chr4:160199000-160202400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr4:160199800-160205000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:160200000-160202800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:160200200-160202800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:160200400-160202400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr4:160200400-160203000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:160200600-160203000	Weak transcription	Brain Angular Gyrus	brain
50	chr4:160200600-160203600	Weak transcription	Brain Substantia Nigra	brain

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