Variant report

Variant	rs10516430
Chromosome Location	chr4:99337881-99337882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10010718	0.84[JPT][hapmap]
rs10516428	0.87[JPT][hapmap]
rs12508978	0.87[JPT][hapmap]
rs13103626	0.89[MEX][hapmap];0.90[YRI][hapmap]
rs13116916	0.81[JPT][hapmap];0.80[YRI][hapmap]
rs17027523	0.84[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs17027570	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34271573	0.84[ASN][1000 genomes]
rs34489597	0.83[ASN][1000 genomes]
rs35038036	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4496588	0.84[ASN][1000 genomes]
rs57246256	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7671104	0.87[JPT][hapmap]
rs7678647	0.87[JPT][hapmap]
rs9884594	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Biochemical measures	19260141	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10516430	RAP1GDS1	cis	multi-tissue	Pritchard
rs10516430	ADH6	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99264200-99338200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:99288400-99342400	Weak transcription	A549	lung
3	chr4:99290600-99346000	Weak transcription	Fetal Lung	lung
4	chr4:99299400-99350800	Weak transcription	NHLF	lung
5	chr4:99299600-99338200	Weak transcription	NHDF-Ad	bronchial
6	chr4:99307000-99366200	Weak transcription	Fetal Brain Male	brain
7	chr4:99308600-99363200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:99312000-99355400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:99317600-99342200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:99317800-99342800	Weak transcription	HSMMtube	muscle
11	chr4:99319200-99341800	Weak transcription	HMEC	breast
12	chr4:99325800-99367000	Weak transcription	Right Ventricle	heart
13	chr4:99326400-99342200	Weak transcription	Brain Angular Gyrus	brain
14	chr4:99327800-99355400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:99330800-99342200	Weak transcription	Brain Substantia Nigra	brain
16	chr4:99331000-99338000	Weak transcription	HSMM	muscle
17	chr4:99333400-99342200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:99333800-99342200	Weak transcription	Brain Anterior Caudate	brain
19	chr4:99334000-99338000	Weak transcription	Liver	Liver
20	chr4:99334000-99339000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr4:99334000-99339800	Weak transcription	Fetal Stomach	stomach
22	chr4:99334000-99342200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:99334000-99355000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:99334200-99338000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:99334200-99338000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:99334200-99338000	Weak transcription	Primary T cells from cord blood	blood
27	chr4:99334200-99338400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:99334200-99338800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:99334200-99339200	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:99334200-99339800	Weak transcription	Ovary	ovary
31	chr4:99334200-99339800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:99334200-99340000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:99334200-99342000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:99334200-99342000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:99334200-99342200	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:99334200-99342200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:99334200-99342400	Weak transcription	Pancreas	Pancrea
38	chr4:99334200-99342400	Weak transcription	GM12878-XiMat	blood
39	chr4:99334200-99345000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:99334200-99350800	Weak transcription	NHEK	skin
41	chr4:99334200-99355200	Weak transcription	Fetal Kidney	kidney
42	chr4:99334200-99355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:99334400-99338000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:99334400-99338000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:99334400-99338000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:99334400-99338000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr4:99334400-99338000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:99334400-99338000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:99334400-99338000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:99334400-99338000	Weak transcription	Fetal Thymus	thymus

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