Variant report

Variant	rs2278133
Chromosome Location	chr15:31353388-31353389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10162731	0.81[ASN][1000 genomes]
rs1035705	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs10851487	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs11070764	0.91[ASN][1000 genomes]
rs11070767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636121	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1991214	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2288241	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2288242	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs2338834	0.83[CHD][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs2338835	0.85[ASN][1000 genomes]
rs2911849	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2911850	0.85[ASN][1000 genomes]
rs2911851	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2911853	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2911854	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2959041	0.81[ASN][1000 genomes]
rs2959042	0.81[ASN][1000 genomes]
rs3743234	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs4779501	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4779808	0.81[ASN][1000 genomes]
rs4779810	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4779811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs4779812	0.87[EUR][1000 genomes]
rs4779813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165995	0.81[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7173280	0.83[CHD][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs7173932	0.81[ASN][1000 genomes]
rs7174338	0.81[ASN][1000 genomes]
rs7174872	0.81[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7179304	0.85[ASN][1000 genomes]
rs8037421	0.81[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8041204	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
10	nsv903835	chr15:31312743-31384797	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv903836	chr15:31330280-31512652	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
12	nsv431373	chr15:31341461-31369498	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	12 gene(s)	inside rSNPs	n/a
13	nsv431372	chr15:31341461-31409090	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv1036010	chr15:31348902-31375379	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	12 gene(s)	inside rSNPs	n/a
15	nsv1040840	chr15:31348902-31412706	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
16	nsv542316	chr15:31348902-31412706	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
17	nsv1046535	chr15:31352063-31392141	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2278133	GABRG3	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31343600-31355400	Weak transcription	Spleen	Spleen
2	chr15:31351400-31360000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:31352000-31353600	Enhancers	Pancreas	Pancrea
4	chr15:31352200-31353600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:31352200-31353600	Enhancers	Gastric	stomach
6	chr15:31352800-31353400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:31352800-31353600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:31352800-31355600	Enhancers	Fetal Brain Male	brain
9	chr15:31353000-31353600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:31353000-31353800	Enhancers	Left Ventricle	heart
11	chr15:31353000-31355600	Enhancers	Brain Germinal Matrix	brain
12	chr15:31353200-31353400	Weak transcription	Fetal Kidney	kidney
13	chr15:31353200-31354400	Weak transcription	Esophagus	oesophagus
14	chr15:31353200-31363400	Weak transcription	Right Atrium	heart

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