Variant report

Variant	rs13118519
Chromosome Location	chr4:141851355-141851356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10004141	0.88[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10004146	0.88[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10009037	0.88[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs10009916	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11100687	0.83[AFR][1000 genomes]
rs11732171	0.89[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs11735133	0.89[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs11735986	0.88[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11930379	0.84[EUR][1000 genomes]
rs12503723	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12511709	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12642167	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12649305	0.84[AFR][1000 genomes]
rs13111614	0.89[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs13111885	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs13120735	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13131785	0.82[AFR][1000 genomes]
rs13135760	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13138724	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13144869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425440	0.81[CEU][hapmap]
rs1425441	0.85[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1425447	0.89[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1541735	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17338560	0.85[CEU][hapmap]
rs17338710	0.88[CEU][hapmap]
rs28445329	0.81[AFR][1000 genomes]
rs4388161	0.83[AFR][1000 genomes]
rs6537018	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6537019	0.89[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6537020	0.87[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6537021	0.89[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6827543	0.86[AFR][1000 genomes]
rs6829247	0.89[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6838120	0.81[AFR][1000 genomes]
rs6848867	0.86[AFR][1000 genomes]
rs6856531	0.86[AFR][1000 genomes]
rs7656504	0.90[AFR][1000 genomes]
rs7662414	0.89[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs7678079	0.88[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7683060	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7686712	0.94[AFR][1000 genomes]
rs874774	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv830090	chr4:141770494-141947764	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830091	chr4:141796603-141980546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv880168	chr4:141826780-141900370	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13118519	RNF150	cis	cerebellum	SCAN
rs13118519	SNORA38B	trans	cerebellum	SCAN
rs13118519	RAB33B	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:141816200-141851400	Weak transcription	Brain Anterior Caudate	brain
2	chr4:141823200-141855800	Weak transcription	Osteobl	bone
3	chr4:141832200-141855200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:141842800-141852200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:141843200-141853400	Weak transcription	Fetal Brain Female	brain
6	chr4:141846400-141855200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:141846600-141855600	Weak transcription	Fetal Brain Male	brain
8	chr4:141846800-141853200	Weak transcription	Spleen	Spleen
9	chr4:141847000-141851600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:141847200-141855200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:141847200-141855200	Weak transcription	Ovary	ovary
12	chr4:141847200-141855800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:141847400-141855200	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:141847400-141855200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:141848000-141851400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:141848200-141851400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:141848200-141856400	Weak transcription	NH-A	brain
18	chr4:141848200-141860600	Weak transcription	Aorta	Aorta
19	chr4:141848400-141851400	Weak transcription	Fetal Heart	heart
20	chr4:141848600-141851600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:141849600-141851600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:141850000-141857400	Enhancers	Colon Smooth Muscle	Colon
23	chr4:141850400-141855400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:141850400-141855800	Weak transcription	Adipose Nuclei	Adipose
25	chr4:141850400-141856200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:141850800-141851600	Enhancers	Right Ventricle	heart
27	chr4:141850800-141851800	Enhancers	Left Ventricle	heart
28	chr4:141850800-141852200	Enhancers	Psoas Muscle	Psoas
29	chr4:141850800-141853000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:141851000-141851800	Enhancers	Stomach Smooth Muscle	stomach
31	chr4:141851200-141851400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:141851200-141851800	Enhancers	Right Atrium	heart
33	chr4:141851200-141852200	Strong transcription	Fetal Stomach	stomach

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