Variant report

Variant	rs7686393
Chromosome Location	chr4:47558154-47558155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10003620	0.95[ASN][1000 genomes]
rs10006939	0.95[ASN][1000 genomes]
rs10034504	0.95[ASN][1000 genomes]
rs10938490	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10938491	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10938492	0.94[ASN][1000 genomes]
rs10938493	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11723676	0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs11728366	0.95[ASN][1000 genomes]
rs11728642	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11729212	0.95[ASN][1000 genomes]
rs11729247	0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs11729252	0.91[JPT][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs11730590	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498466	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12500474	0.95[ASN][1000 genomes]
rs12502166	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12502321	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12502323	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12507138	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12507737	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12507939	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13105858	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13106043	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110314	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13122990	0.95[ASN][1000 genomes]
rs13123471	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13123704	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13125264	0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs13134125	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13151340	0.95[ASN][1000 genomes]
rs16851681	0.84[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs17462424	0.81[MEX][hapmap]
rs28414421	0.95[ASN][1000 genomes]
rs28535313	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34442412	0.95[ASN][1000 genomes]
rs34707051	0.95[ASN][1000 genomes]
rs34872589	0.95[ASN][1000 genomes]
rs3922408	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3924898	0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3924899	0.95[ASN][1000 genomes]
rs3924900	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4298115	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4391005	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4694857	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.99[ASN][1000 genomes]
rs6810449	0.90[ASN][1000 genomes]
rs6811048	0.95[ASN][1000 genomes]
rs6823365	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6825063	0.81[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6827604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[ASN][1000 genomes]
rs6829677	0.93[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6832417	0.95[ASN][1000 genomes]
rs6840205	0.81[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6842577	0.95[ASN][1000 genomes]
rs6843438	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6851221	0.81[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs7687166	0.81[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs7695942	1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs9995068	0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.92[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	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7686393	GABRA2	cis	cerebellum	SCAN
rs7686393	NIPAL1	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47488800-47559800	Weak transcription	Right Ventricle	heart
2	chr4:47512400-47577200	Weak transcription	Small Intestine	intestine
3	chr4:47526400-47559800	Weak transcription	Pancreas	Pancrea
4	chr4:47534000-47559800	Weak transcription	Lung	lung
5	chr4:47534400-47560000	Weak transcription	Brain Substantia Nigra	brain
6	chr4:47534400-47560400	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:47534600-47559600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:47534600-47580800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:47534600-47592000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:47536200-47571000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:47538600-47566800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:47538800-47571000	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:47539600-47589000	Weak transcription	Colonic Mucosa	Colon
14	chr4:47541000-47571000	Weak transcription	Spleen	Spleen
15	chr4:47542200-47563400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:47542800-47559800	Weak transcription	HUVEC	blood vessel
17	chr4:47544800-47574000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:47545400-47566800	Strong transcription	Placenta	Placenta
19	chr4:47545600-47559800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:47546400-47589400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:47547200-47564200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:47547800-47558200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:47548800-47583800	Weak transcription	Psoas Muscle	Psoas
24	chr4:47549000-47559800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:47549000-47574000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:47549400-47559600	Weak transcription	Aorta	Aorta
27	chr4:47549400-47559600	Weak transcription	Brain Angular Gyrus	brain
28	chr4:47549400-47563000	Weak transcription	Fetal Heart	heart
29	chr4:47549400-47566800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:47549400-47570800	Weak transcription	Esophagus	oesophagus
31	chr4:47549400-47570800	Weak transcription	NHLF	lung
32	chr4:47549400-47573600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:47549400-47574800	Weak transcription	Primary T cells from cord blood	blood
34	chr4:47549400-47576800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:47549600-47570800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:47550600-47559600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:47550600-47559800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:47550800-47566800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:47551200-47559800	Weak transcription	GM12878-XiMat	blood
40	chr4:47551400-47559600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:47551400-47559800	Weak transcription	Gastric	stomach
42	chr4:47551400-47560000	Weak transcription	Fetal Lung	lung
43	chr4:47551800-47559800	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:47552000-47562600	Weak transcription	Fetal Kidney	kidney
45	chr4:47552200-47559800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:47553000-47559800	Weak transcription	Adipose Nuclei	Adipose
47	chr4:47553000-47570800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:47553800-47558400	Strong transcription	HSMM	muscle
49	chr4:47553800-47559800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:47554000-47566800	Weak transcription	NHDF-Ad	bronchial

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