Variant report

Variant	rs4956518
Chromosome Location	chr4:142048547-142048548
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10028355	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1003257	1.00[CHB][hapmap]
rs1027815	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519584	0.82[GIH][hapmap];0.82[MEX][hapmap]
rs10519586	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12509440	0.86[GIH][hapmap]
rs1364881	1.00[CHB][hapmap]
rs1425445	1.00[CHB][hapmap]
rs1507178	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17340802	1.00[CHB][hapmap]
rs17425151	1.00[CHB][hapmap]
rs187139	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs189568	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1899424	1.00[CHB][hapmap]
rs2033612	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs354939	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs354941	0.96[EUR][1000 genomes]
rs3913899	0.86[GIH][hapmap];0.82[MEX][hapmap]
rs4123363	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4245936	1.00[CHB][hapmap]
rs4629541	0.86[GIH][hapmap]
rs4956515	1.00[EUR][1000 genomes]
rs4956516	1.00[EUR][1000 genomes]
rs4956517	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs62324904	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62324905	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6537024	1.00[CHB][hapmap]
rs6537030	0.86[GIH][hapmap]
rs6835953	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6853785	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72724492	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7665647	1.00[CHB][hapmap]
rs7669929	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7683490	0.86[GIH][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880167	chr4:141616979-142092124	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv880170	chr4:142046828-142137165	Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv526770	chr4:142048547-142061946	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4956518	MGST2	cis	cerebellum	SCAN
rs4956518	INPP4B	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142038600-142052600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:142039000-142049200	Weak transcription	Fetal Brain Female	brain
3	chr4:142039400-142051800	Weak transcription	Aorta	Aorta
4	chr4:142041000-142048600	Weak transcription	Adipose Nuclei	Adipose
5	chr4:142041000-142052200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:142042600-142048600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:142043600-142051800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:142044400-142051200	Weak transcription	Osteobl	bone
9	chr4:142044600-142051600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:142044800-142051800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:142045800-142048800	Enhancers	Fetal Heart	heart
12	chr4:142045800-142049000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:142045800-142051200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:142045800-142051200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:142047000-142048600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr4:142047200-142048800	Weak transcription	Brain Substantia Nigra	brain
17	chr4:142047200-142049400	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr4:142047200-142050200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr4:142047400-142048600	Enhancers	Psoas Muscle	Psoas
20	chr4:142047400-142048800	Enhancers	Right Ventricle	heart
21	chr4:142047400-142049000	Enhancers	Stomach Smooth Muscle	stomach
22	chr4:142047400-142049400	Enhancers	Left Ventricle	heart
23	chr4:142047400-142049600	Enhancers	Ovary	ovary
24	chr4:142047600-142048800	Enhancers	Right Atrium	heart
25	chr4:142047600-142049600	Enhancers	Fetal Stomach	stomach
26	chr4:142047600-142050600	Enhancers	Colon Smooth Muscle	Colon
27	chr4:142047800-142048800	Weak transcription	Brain Anterior Caudate	brain
28	chr4:142048000-142048600	Enhancers	Fetal Brain Male	brain
29	chr4:142048200-142049200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:142048200-142051800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:142048400-142049000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:142048400-142049000	Weak transcription	Spleen	Spleen
33	chr4:142048400-142049200	Weak transcription	Lung	lung
34	chr4:142048400-142050400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr4:142048400-142050600	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:142048400-142053000	Weak transcription	Pancreas	Pancrea

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