Variant report

Variant	rs7930830
Chromosome Location	chr11:107882823-107882824
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:107878216..107881089-chr11:107881577..107884403,2	MCF-7	breast:
2	chr11:107879275..107881405-chr11:107882359..107886354,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166266	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10749914	0.82[CEU][hapmap]
rs10789651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890800	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890802	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10890803	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890804	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890805	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890806	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10890808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11212491	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212505	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11212524	0.82[CEU][hapmap]
rs2271852	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3741051	0.83[EUR][1000 genomes]
rs3858395	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3950984	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4503496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4568970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568971	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4575229	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754286	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117111	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130999	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926222	0.82[CEU][hapmap]
rs7935911	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947410	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1039425	chr11:107468681-107895836	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv521771	chr11:107590335-107904646	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1048938	chr11:107604473-107929950	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv2750980	chr11:107720941-107970986	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1047984	chr11:107794729-107950746	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1040345	chr11:107824764-107924309	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7930830	GRIA4	cis	parietal	SCAN
rs7930830	NPAT	cis	parietal	SCAN
rs7930830	PDCD1LG2	trans	parietal	SCAN
rs7930830	ACAT1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107879000-107885200	Active TSS	GM12878-XiMat	blood
2	chr11:107880800-107883400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:107880800-107883600	Weak transcription	Spleen	Spleen
4	chr11:107880800-107888400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:107880800-107890600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:107881000-107883200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:107881000-107883400	Weak transcription	Gastric	stomach
8	chr11:107881000-107883400	Weak transcription	Left Ventricle	heart
9	chr11:107881000-107883600	Weak transcription	Esophagus	oesophagus
10	chr11:107881000-107883800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:107881000-107884800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:107881000-107885000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr11:107881000-107886200	Weak transcription	Pancreas	Pancrea
14	chr11:107881000-107891000	Weak transcription	Lung	lung
15	chr11:107881000-107904000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr11:107881000-107904800	Weak transcription	Placenta	Placenta
17	chr11:107881200-107883200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr11:107881200-107883800	Enhancers	Small Intestine	intestine
19	chr11:107881200-107884400	Enhancers	Fetal Brain Male	brain
20	chr11:107881200-107884800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:107881200-107885000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr11:107881200-107885200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr11:107881200-107885200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr11:107881200-107886800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:107881200-107887200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:107881200-107890000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:107881200-107890600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:107881400-107883000	Weak transcription	Right Ventricle	heart
29	chr11:107881400-107883200	Enhancers	Brain Cingulate Gyrus	brain
30	chr11:107881400-107883800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr11:107881400-107884800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr11:107881400-107885000	Enhancers	Brain Anterior Caudate	brain
33	chr11:107881600-107883000	Enhancers	Primary B cells from cord blood	blood
34	chr11:107881600-107884000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:107881600-107884200	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:107881600-107884400	Enhancers	Primary T cells from cord blood	blood
37	chr11:107881600-107884800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:107881600-107885000	Enhancers	Adipose Nuclei	Adipose
39	chr11:107881600-107896200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:107881600-107904600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:107881800-107883800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr11:107881800-107884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:107881800-107884200	Weak transcription	Aorta	Aorta
44	chr11:107881800-107884400	Weak transcription	Fetal Thymus	thymus
45	chr11:107881800-107884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:107881800-107884800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:107881800-107885600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:107881800-107890400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:107882000-107883600	Weak transcription	Brain Angular Gyrus	brain
50	chr11:107882000-107884000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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