Variant report

Variant	rs10028181
Chromosome Location	chr4:54000949-54000950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10003612	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008792	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10016471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11133243	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11133244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11936236	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17082398	0.83[JPT][hapmap]
rs28497299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35275015	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3849654	0.83[JPT][hapmap]
rs4241973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4616822	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66506011	0.83[ASN][1000 genomes]
rs71621063	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7378381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10028181	KIT	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53978800-54008000	Weak transcription	Primary T cells from cord blood	blood
2	chr4:53986800-54010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:53986800-54011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:53987800-54016800	Weak transcription	NHLF	lung
5	chr4:53988200-54008000	Weak transcription	Primary B cells from cord blood	blood
6	chr4:53988600-54011000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:53989200-54010200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr4:53992400-54009600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:53993800-54027800	Weak transcription	Fetal Stomach	stomach
10	chr4:53994000-54011000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:53995200-54014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:53995400-54017800	Weak transcription	Brain Substantia Nigra	brain
13	chr4:53997000-54017600	Weak transcription	Gastric	stomach
14	chr4:53997400-54020000	Weak transcription	HSMM	muscle
15	chr4:53997800-54011000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:53998000-54008600	Weak transcription	Ovary	ovary
17	chr4:53998000-54010800	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:53998000-54011000	Weak transcription	Left Ventricle	heart
19	chr4:53998400-54010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:53998600-54014400	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:53998800-54010400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:53999000-54010200	Weak transcription	Osteobl	bone
23	chr4:53999000-54011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:53999000-54013200	Weak transcription	Brain Angular Gyrus	brain
25	chr4:53999000-54017200	Weak transcription	Fetal Lung	lung
26	chr4:53999000-54027800	Weak transcription	NHDF-Ad	bronchial
27	chr4:53999200-54001400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:53999200-54003800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:53999200-54009600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr4:53999200-54011000	Weak transcription	Adipose Nuclei	Adipose
31	chr4:54000200-54003200	Weak transcription	GM12878-XiMat	blood

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