Variant report

Variant	rs4788559
Chromosome Location	chr16:71848959-71848960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71842099..71845312-chr16:71845371..71851524,8	K562	blood:
2	chr16:71847353..71849880-chr16:71853072..71855463,2	MCF-7	breast:
3	chr16:71815919..71817496-chr16:71847689..71850509,2	MCF-7	breast:
4	chr16:71843164..71845312-chr16:71848079..71849658,2	K562	blood:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11075901	0.89[ASW][hapmap];0.90[CEU][hapmap];0.89[LWK][hapmap];0.83[TSI][hapmap]
rs11075904	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs11075905	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862723	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs12929547	0.90[EUR][1000 genomes]
rs1392484	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1423983	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs2032918	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap]
rs2052585	0.95[CEU][hapmap]
rs2133773	0.91[EUR][1000 genomes]
rs2334877	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4788444	0.83[EUR][1000 genomes]
rs4788548	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs4788550	0.80[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs4788553	0.85[EUR][1000 genomes]
rs4788557	0.87[EUR][1000 genomes]
rs4788828	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs6499528	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs6499530	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs6499534	0.82[EUR][1000 genomes]
rs6499538	0.85[CEU][hapmap];1.00[CHD][hapmap];0.81[EUR][1000 genomes]
rs6499540	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7186112	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7188675	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs7193549	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs7195059	0.90[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap]
rs7201712	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7202479	0.81[EUR][1000 genomes]
rs7204118	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7204608	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap]
rs7204967	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7206470	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap]
rs7359478	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8044144	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8052910	0.89[EUR][1000 genomes]
rs8053186	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8055419	0.86[EUR][1000 genomes]
rs889568	0.81[EUR][1000 genomes]
rs9635524	0.84[EUR][1000 genomes]
rs979790	1.00[CHD][hapmap]
rs9929840	0.95[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs9929985	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9930015	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs9934301	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9937511	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9939458	0.90[CEU][hapmap]

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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4788559	COG4	cis	parietal	SCAN
rs4788559	PHLPP2	cis	Muscle Skeletal	GTEx
rs4788559	CBFB	cis	parietal	SCAN
rs4788559	B3GNT9	cis	parietal	SCAN
rs4788559	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx
rs4788559	CTCF	cis	cerebellum	SCAN
rs4788559	ZNF23	cis	parietal	SCAN
rs4788559	NRN1L	cis	parietal	SCAN
rs4788559	RANBP10	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71843600-71852600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:71843800-71850000	Weak transcription	Osteobl	bone
3	chr16:71843800-71850400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:71843800-71850400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:71843800-71850400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr16:71843800-71850400	Weak transcription	Fetal Stomach	stomach
7	chr16:71843800-71850600	Weak transcription	Brain Hippocampus Middle	brain
8	chr16:71843800-71850600	Weak transcription	A549	lung
9	chr16:71843800-71850800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr16:71843800-71850800	Weak transcription	HSMM	muscle
11	chr16:71843800-71851600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr16:71843800-71851600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr16:71843800-71855400	Weak transcription	Primary T cells from cord blood	blood
14	chr16:71843800-71861600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr16:71844000-71850400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr16:71844000-71859400	Weak transcription	Fetal Intestine Small	intestine
17	chr16:71844200-71849600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr16:71844200-71850400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr16:71844200-71850400	Weak transcription	Hela-S3	cervix
20	chr16:71844200-71850600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr16:71844200-71850600	Weak transcription	Brain Angular Gyrus	brain
22	chr16:71844200-71862200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr16:71844400-71850000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr16:71844800-71862000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr16:71845200-71851800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr16:71845400-71849600	Weak transcription	GM12878-XiMat	blood
27	chr16:71845400-71850600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr16:71845600-71850600	Weak transcription	K562	blood
29	chr16:71845600-71851600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr16:71846200-71850400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr16:71846200-71850600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr16:71846600-71851600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr16:71848600-71852200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:71848800-71849600	Enhancers	HepG2	liver

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