Variant report

Variant	rs28279
Chromosome Location	chr16:11968555-11968556
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:11835919..11837744-chr16:11966699..11968629,2	MCF-7	breast:
2	chr16:11959980..11962642-chr16:11968005..11970163,2	K562	blood:
3	chr16:11968165..11970950-chr16:11974368..11976802,2	K562	blood:

Variant related genes	Relation type
ENSG00000153066	Chromatin interaction
ENSG00000261560	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11646545	0.83[CEU][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11647818	0.84[ASN][1000 genomes]
rs12925740	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs153025	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154148	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs171656	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075159	0.87[EUR][1000 genomes]
rs251723	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33619	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33620	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33623	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33631	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33635	0.88[TSI][hapmap]
rs33637	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33639	0.81[CHD][hapmap]
rs33640	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33643	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33645	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33647	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33648	0.82[EUR][1000 genomes]
rs33649	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33651	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33652	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33653	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33654	0.82[EUR][1000 genomes]
rs33655	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33659	0.87[CHD][hapmap]
rs33660	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35153773	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40311	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4511557	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs718081	0.83[JPT][hapmap]
rs7185589	0.84[ASN][1000 genomes]
rs7198817	0.84[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7202234	0.84[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs8046617	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8047726	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8061189	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv984257	chr16:11968206-11992901	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28279	RSL1D1	cis	parietal	SCAN
rs28279	TNFRSF17	cis	parietal	SCAN
rs28279	GSPT1	Cis_1M	lymphoblastoid	RTeQTL
rs28279	TNFRSF17	cis	cerebellum	SCAN
rs28279	NDE1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11946200-11975600	Weak transcription	Aorta	Aorta
2	chr16:11946400-11969400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:11946400-11969400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr16:11946400-11969400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:11946400-11975600	Weak transcription	Esophagus	oesophagus
6	chr16:11946600-11969000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:11946600-11970400	Weak transcription	Right Atrium	heart
8	chr16:11947000-11969400	Weak transcription	Right Ventricle	heart
9	chr16:11947200-11968800	Weak transcription	Ovary	ovary
10	chr16:11948400-11969000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr16:11948600-11969000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr16:11948800-11969400	Weak transcription	Brain Angular Gyrus	brain
13	chr16:11948800-11970200	Weak transcription	Gastric	stomach
14	chr16:11958800-11969200	Weak transcription	Psoas Muscle	Psoas
15	chr16:11959400-11969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr16:11960600-11969400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr16:11960600-11969600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr16:11961200-11972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr16:11961400-11975600	Weak transcription	Pancreas	Pancrea
20	chr16:11961600-11971600	Strong transcription	NHDF-Ad	bronchial
21	chr16:11961600-11986000	Weak transcription	Stomach Mucosa	stomach
22	chr16:11961800-11969400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr16:11961800-11972400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr16:11961800-11991000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr16:11962000-11992200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr16:11962000-11994600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr16:11962200-11970200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr16:11962200-11992000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr16:11962400-11971800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr16:11962400-11972800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr16:11962400-11982600	Strong transcription	Fetal Thymus	thymus
32	chr16:11962400-11984000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr16:11962400-11990800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr16:11962400-11992000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr16:11962400-11992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr16:11962400-11992200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr16:11962400-11992400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr16:11962400-11995000	Strong transcription	Dnd41	blood
39	chr16:11962600-11971200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr16:11962600-11985600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr16:11962600-11990600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr16:11962600-11991800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr16:11963000-11971000	Strong transcription	Hela-S3	cervix
45	chr16:11963200-11970800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr16:11963400-11969400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr16:11963400-11972600	Strong transcription	K562	blood
48	chr16:11963400-11975000	Weak transcription	Fetal Kidney	kidney
49	chr16:11963600-11968800	Weak transcription	NHLF	lung
50	chr16:11963800-11969400	Weak transcription	Brain Anterior Caudate	brain

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