Variant report

Variant	rs3866959
Chromosome Location	chr17:17173531-17173532
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17172337..17174059-chr17:17181863..17184662,2	MCF-7	breast:
2	chr17:17171742..17173739-chr17:17174363..17176505,2	K562	blood:
3	chr17:17172008..17173740-chr17:17177351..17179139,2	K562	blood:
4	chr17:17162011..17164350-chr17:17171227..17174185,2	K562	blood:

Variant related genes	Relation type
ENSG00000141030	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12453455	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600589	0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12949822	0.81[ASN][1000 genomes]
rs1630656	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708617	0.94[ASN][1000 genomes]
rs1708621	0.94[ASN][1000 genomes]
rs1708624	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1708625	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1708628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1736204	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736205	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1736208	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1736209	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1736211	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736212	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736216	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1736217	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs1736221	0.93[ASN][1000 genomes]
rs2012954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2018781	0.94[ASN][1000 genomes]
rs2292527	0.92[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2472689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36079048	0.90[ASN][1000 genomes]
rs4985760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066065	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62066066	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6502564	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6502568	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502569	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502570	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502571	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217560	0.80[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7220577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220827	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs7221553	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7224598	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7225876	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066090	0.94[ASN][1000 genomes]
rs8080386	0.92[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9892352	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894565	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.94[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	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3866959	COPS3	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17148600-17178800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:17148600-17179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:17148600-17179600	Strong transcription	Fetal Muscle Trunk	muscle
4	chr17:17148600-17180000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:17148800-17178400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:17148800-17178400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:17148800-17179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:17148800-17179600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:17148800-17179600	Strong transcription	Fetal Muscle Leg	muscle
10	chr17:17148800-17179800	Strong transcription	Fetal Stomach	stomach
11	chr17:17148800-17180200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:17148800-17180400	Strong transcription	Fetal Thymus	thymus
13	chr17:17149000-17174800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:17149000-17174800	Strong transcription	Adipose Nuclei	Adipose
15	chr17:17149000-17174800	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr17:17149000-17178400	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr17:17149000-17178800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:17149000-17179200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:17149000-17179400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:17149000-17180800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:17149000-17181200	Strong transcription	Dnd41	blood
22	chr17:17149200-17177400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr17:17149200-17179000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:17149200-17179600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr17:17149200-17179600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr17:17149200-17179800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr17:17149400-17174400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr17:17149400-17175000	Strong transcription	Thymus	Thymus
29	chr17:17149400-17179600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr17:17149400-17179600	Strong transcription	Placenta	Placenta
31	chr17:17149600-17174800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr17:17149800-17179000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr17:17150000-17180000	Strong transcription	Primary T cells from cord blood	blood
34	chr17:17150200-17179400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr17:17150200-17179800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:17153400-17174800	Strong transcription	Fetal Intestine Large	intestine
37	chr17:17153600-17178000	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr17:17155000-17179800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:17155200-17174800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr17:17156800-17179600	Strong transcription	Liver	Liver
41	chr17:17157200-17175000	Strong transcription	A549	lung
42	chr17:17157600-17179600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr17:17157800-17177600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:17159800-17179600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr17:17160400-17181800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:17160800-17179400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr17:17162200-17177400	Strong transcription	Fetal Lung	lung
48	chr17:17162200-17179400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr17:17163600-17173800	Weak transcription	Stomach Mucosa	stomach
50	chr17:17163600-17182600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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