Variant report

Variant	rs33639
Chromosome Location	chr16:11989499-11989500
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:11988100..11996073-chr16:12007143..12011577,10	MCF-7	breast:
2	chr16:11988764..11995180-chr16:12006980..12012068,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266163	Chromatin interaction
ENSG00000103342	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1019813	0.89[CEU][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1019814	0.89[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1029285	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852344	0.89[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11075027	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11075030	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11075032	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11075033	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11544193	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11639888	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11641520	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11645213	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11645811	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11647580	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11649623	0.87[ASN][1000 genomes]
rs12149833	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12444127	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs154149	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17235629	0.85[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17236573	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2192645	0.92[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2215928	0.88[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2288547	0.80[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28279	0.81[CHD][hapmap]
rs28567665	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28653099	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33619	0.86[ASW][hapmap];0.81[CHD][hapmap];0.80[MEX][hapmap]
rs33623	0.86[ASW][hapmap];0.84[CHD][hapmap];0.80[MEX][hapmap]
rs33636	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33650	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs33657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33659	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33660	0.88[CHD][hapmap];0.80[MEX][hapmap]
rs40311	0.88[CHD][hapmap];0.80[MEX][hapmap]
rs62038777	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62038793	0.88[ASN][1000 genomes]
rs62038798	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6498251	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs718080	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7189510	0.85[ASN][1000 genomes]
rs7198817	0.81[CHD][hapmap];0.80[MEX][hapmap]
rs7202065	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9673473	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9925010	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9927446	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9938242	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	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
5	nsv1735	chr16:11986963-12031597	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs33639	NDE1	cis	parietal	SCAN
rs33639	TNFRSF17	cis	parietal	SCAN
rs33639	TNFRSF17	cis	cerebellum	SCAN
rs33639	GSPT1	Cis_1M	lymphoblastoid	RTeQTL
rs33639	RSL1D1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11961800-11991000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:11962000-11992200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr16:11962000-11994600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:11962200-11992000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr16:11962400-11990800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:11962400-11992000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr16:11962400-11992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:11962400-11992200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:11962400-11992400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr16:11962400-11995000	Strong transcription	Dnd41	blood
11	chr16:11962600-11990600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:11962600-11991800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:11964800-11990800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:11964800-11991000	Strong transcription	Fetal Intestine Large	intestine
16	chr16:11965000-11990200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr16:11965000-11991000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr16:11965200-11991000	Strong transcription	GM12878-XiMat	blood
19	chr16:11965400-11990800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr16:11965400-11991400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr16:11965600-11991000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr16:11965800-11990200	Strong transcription	Liver	Liver
23	chr16:11965800-11995000	Strong transcription	HepG2	liver
24	chr16:11966000-11991000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr16:11966000-11991400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:11966200-12006200	Weak transcription	Fetal Heart	heart
27	chr16:11966600-11991000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr16:11967000-11990200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:11969000-11989600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr16:11969200-11990600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr16:11971600-11995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr16:11972000-11990400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr16:11972000-11991000	Strong transcription	Thymus	Thymus
34	chr16:11972200-11989600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:11972400-11991000	Strong transcription	Adipose Nuclei	Adipose
36	chr16:11973000-11990400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:11973200-11989600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr16:11973400-11990200	Strong transcription	Osteobl	bone
39	chr16:11973600-11990400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr16:11973800-11991000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr16:11973800-11991000	Strong transcription	Primary T cells from cord blood	blood
42	chr16:11974400-11990000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr16:11974600-11991200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr16:11976600-12004800	Weak transcription	Esophagus	oesophagus
45	chr16:11977000-12007200	Weak transcription	Colonic Mucosa	Colon
46	chr16:11977200-12004600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr16:11979800-12003200	Weak transcription	Small Intestine	intestine
48	chr16:11981000-11990800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr16:11981200-11990400	Weak transcription	Brain Hippocampus Middle	brain
50	chr16:11981200-12004000	Weak transcription	Brain Cingulate Gyrus	brain

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