Variant report

Variant	rs1131773
Chromosome Location	chr9:95840256-95840257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10821066	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992622	0.89[CHD][hapmap]
rs10992623	0.89[CHD][hapmap]
rs10992626	0.94[ASN][1000 genomes]
rs10992628	0.89[ASN][1000 genomes]
rs12004054	0.90[ASN][1000 genomes]
rs12352182	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12375973	0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12378451	0.90[JPT][hapmap]
rs16908779	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1970623	0.86[JPT][hapmap]
rs28468656	0.93[ASN][1000 genomes]
rs4077176	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4077177	0.85[CHD][hapmap]
rs4077811	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4078501	0.83[ASN][1000 genomes]
rs4341217	0.92[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4636265	0.96[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4743886	0.86[JPT][hapmap]
rs56000948	0.94[EUR][1000 genomes]
rs57866297	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61478314	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479450	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7025686	0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7036869	0.89[CHD][hapmap]
rs7046192	0.83[CEU][hapmap];0.88[CHD][hapmap];0.81[EUR][1000 genomes]
rs7046328	0.81[LWK][hapmap]
rs7849306	0.94[ASN][1000 genomes]
rs7859109	1.00[CEU][hapmap];0.93[CHD][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7870697	0.94[EUR][1000 genomes]
rs7870953	0.81[EUR][1000 genomes]
rs9695137	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9696341	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9696357	0.89[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer 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 target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1131773	GOT2	trans	cerebellum	SCAN
rs1131773	SUSD3	cis	multi-tissue	Pritchard
rs1131773	ZNF484	cis	cerebellum	SCAN
rs1131773	C9orf3	cis	parietal	SCAN
rs1131773	ZNF479	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95824600-95854000	Weak transcription	Gastric	stomach
2	chr9:95828200-95841600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr9:95828600-95845000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr9:95833000-95842800	Weak transcription	GM12878-XiMat	blood
5	chr9:95834400-95857400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:95834800-95846600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:95834800-95848000	Weak transcription	Aorta	Aorta
8	chr9:95835000-95842800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr9:95835400-95843400	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:95835400-95845000	Weak transcription	Lung	lung
11	chr9:95835400-95845400	Weak transcription	Fetal Intestine Large	intestine
12	chr9:95835400-95846400	Weak transcription	Esophagus	oesophagus
13	chr9:95835400-95846600	Weak transcription	Liver	Liver
14	chr9:95835400-95848800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:95835400-95849000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:95835600-95843400	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:95835600-95848000	Weak transcription	Colonic Mucosa	Colon
18	chr9:95836200-95850000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:95836200-95855600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:95836400-95845000	Weak transcription	Fetal Stomach	stomach
21	chr9:95837200-95841000	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr9:95837400-95843200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:95837600-95841400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:95837800-95844200	Strong transcription	Primary T cells from cord blood	blood
25	chr9:95837800-95845000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:95838000-95844600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:95838200-95840400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr9:95838200-95843600	Strong transcription	Spleen	Spleen
29	chr9:95838200-95843800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:95838200-95851000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr9:95838400-95843800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:95838600-95841600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr9:95839000-95841200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr9:95839000-95841600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:95839200-95843600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr9:95839200-95843600	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:95839400-95841600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:95839400-95843200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr9:95839400-95844800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr9:95839600-95845000	Strong transcription	Thymus	Thymus
41	chr9:95839800-95842200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:95839800-95843800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr9:95839800-95851000	Weak transcription	K562	blood
44	chr9:95840000-95840400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr9:95840000-95841400	Weak transcription	Primary B cells from cord blood	blood
46	chr9:95840200-95840400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:95840200-95840400	Strong transcription	Fetal Intestine Small	intestine
48	chr9:95840200-95840400	Strong transcription	Fetal Thymus	thymus
49	chr9:95840200-95840400	Strong transcription	Ovary	ovary
50	chr9:95840200-95841000	Enhancers	Primary hematopoietic stem cells	blood

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