Variant report

Variant	rs3129327
Chromosome Location	chr4:3383674-3383675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10155132	0.96[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10937924	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13104157	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13150241	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071671	0.83[CHB][hapmap]
rs2236052	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs2239725	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap]
rs2748447	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2749778	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2749781	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs2749782	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs2749783	1.00[CEU][hapmap]
rs2749785	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs2798221	0.84[CHB][hapmap]
rs2857982	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3025816	1.00[LWK][hapmap]
rs3129308	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs3129310	1.00[CEU][hapmap]
rs3129328	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129334	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135145	0.96[CEU][hapmap];0.89[CHB][hapmap]
rs3135146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs4690098	1.00[LWK][hapmap]
rs60181496	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60208975	0.85[AMR][1000 genomes]
rs6819202	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7435601	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs881816	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs881817	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs910568	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]

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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3129327	RGS12	cis	cerebellum	SCAN
rs3129327	DGKQ	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3372200-3386400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:3373000-3389000	Weak transcription	Psoas Muscle	Psoas
3	chr4:3373400-3388400	Weak transcription	Fetal Kidney	kidney
4	chr4:3373400-3388800	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:3375000-3389200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:3375200-3387000	Weak transcription	Right Atrium	heart
7	chr4:3375400-3386200	Weak transcription	Right Ventricle	heart
8	chr4:3375400-3386400	Weak transcription	Brain Substantia Nigra	brain
9	chr4:3375400-3386600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:3375400-3389600	Weak transcription	NHLF	lung
11	chr4:3375600-3386200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:3375600-3387000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:3378200-3388800	Weak transcription	Fetal Heart	heart
14	chr4:3378400-3386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:3378400-3388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:3378400-3389000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:3378400-3389200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:3378400-3389200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:3378400-3390400	Weak transcription	Ovary	ovary
20	chr4:3378600-3386200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:3378600-3386400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:3378600-3389600	Weak transcription	Aorta	Aorta
23	chr4:3378800-3386400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:3380800-3386800	Weak transcription	Primary T cells from cord blood	blood
25	chr4:3381000-3389000	Weak transcription	Fetal Brain Male	brain
26	chr4:3381000-3389200	Weak transcription	HSMMtube	muscle
27	chr4:3382200-3386400	Weak transcription	Adipose Nuclei	Adipose
28	chr4:3382200-3386400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:3382200-3386800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:3382400-3386200	Weak transcription	HUVEC	blood vessel
31	chr4:3382400-3386400	Weak transcription	Fetal Intestine Large	intestine
32	chr4:3382400-3386400	Weak transcription	Fetal Lung	lung
33	chr4:3382400-3386400	Weak transcription	Gastric	stomach
34	chr4:3382600-3384000	Weak transcription	Fetal Stomach	stomach
35	chr4:3382600-3384800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:3382600-3386000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:3382600-3386200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr4:3382600-3386200	Weak transcription	Lung	lung
39	chr4:3382600-3386200	Weak transcription	Pancreas	Pancrea
40	chr4:3382600-3386400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:3382600-3386400	Weak transcription	Esophagus	oesophagus
42	chr4:3382600-3386400	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:3382600-3389000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:3382600-3389000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:3382800-3384800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:3382800-3386200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:3383000-3386400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:3383200-3389600	Weak transcription	Fetal Brain Female	brain
49	chr4:3383400-3384400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:3383400-3386000	Weak transcription	Fetal Intestine Small	intestine

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