Variant report

Variant	rs12942295
Chromosome Location	chr17:15973844-15973845
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr17:15973545-15974141	MCF-7	breast:	n/a	n/a
2	FOXM1	chr17:15973568-15974091	MCF-7	breast:	n/a	n/a
3	GATA3	chr17:15973760-15974065	MCF-7	breast:	n/a	n/a
4	POLR2A	chr17:15973699-15973938	K562	blood:	n/a	n/a
5	NR2F2	chr17:15973496-15974158	MCF-7	breast:	n/a	n/a
6	GATA3	chr17:15973568-15974172	MCF-7	breast:	n/a	n/a
7	BACH1	chr17:15973666-15973854	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:7860807..7861740-chr17:15973359..15973862,2	MCF-7	breast:
2	chr17:15081168..15081829-chr17:15973460..15974306,2	MCF-7	breast:
3	chr17:15563102..15563727-chr17:15973385..15973964,2	MCF-7	breast:
4	chr17:15972800..15974994-chr17:15979206..15981179,2	MCF-7	breast:

No data

Variant related genes	Relation type
NCOR1	TF binding region

Extended variants
information (count: 134 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10491104	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1065822	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1075901	0.85[EUR][1000 genomes]
rs1079533	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10852833	0.83[EUR][1000 genomes]
rs11078321	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078327	0.84[EUR][1000 genomes]
rs11078328	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11078330	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078331	0.85[EUR][1000 genomes]
rs11078332	0.83[EUR][1000 genomes]
rs1125156	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1126148	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1160109	0.81[EUR][1000 genomes]
rs11650678	0.83[EUR][1000 genomes]
rs11651290	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11651508	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11652025	0.86[EUR][1000 genomes]
rs11655456	0.81[EUR][1000 genomes]
rs11655773	0.81[EUR][1000 genomes]
rs11656046	0.85[EUR][1000 genomes]
rs11657160	0.85[EUR][1000 genomes]
rs11657912	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11868809	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11869450	0.81[EUR][1000 genomes]
rs11871961	0.90[EUR][1000 genomes]
rs11872032	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12150017	0.83[EUR][1000 genomes]
rs12449895	0.81[EUR][1000 genomes]
rs12451075	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12945463	0.81[EUR][1000 genomes]
rs12945546	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12947205	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12948361	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972503	0.81[EUR][1000 genomes]
rs1989856	0.81[EUR][1000 genomes]
rs2015353	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2041459	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041460	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2051736	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2078050	0.83[EUR][1000 genomes]
rs2157990	0.85[EUR][1000 genomes]
rs2157991	0.85[EUR][1000 genomes]
rs2157992	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2285582	0.85[EUR][1000 genomes]
rs2285583	0.83[EUR][1000 genomes]
rs2301651	0.80[ASN][1000 genomes]
rs2301652	0.80[EUR][1000 genomes]
rs2324084	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2779211	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34236618	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35160872	0.81[EUR][1000 genomes]
rs35168566	0.85[EUR][1000 genomes]
rs36001065	0.86[EUR][1000 genomes]
rs3760297	0.81[EUR][1000 genomes]
rs3760298	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785628	0.85[EUR][1000 genomes]
rs3785629	0.81[EUR][1000 genomes]
rs3785631	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3785633	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815038	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815039	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826360	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4239134	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4435297	0.82[EUR][1000 genomes]
rs4791660	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4791661	0.90[EUR][1000 genomes]
rs4791662	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4792711	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4792712	0.81[EUR][1000 genomes]
rs4792713	0.81[EUR][1000 genomes]
rs4792715	0.81[EUR][1000 genomes]
rs4792716	0.85[EUR][1000 genomes]
rs4792717	0.85[EUR][1000 genomes]
rs4792718	0.82[EUR][1000 genomes]
rs4792719	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55676330	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62073587	0.84[EUR][1000 genomes]
rs6416868	0.81[EUR][1000 genomes]
rs6502482	0.83[EUR][1000 genomes]
rs6502488	0.85[EUR][1000 genomes]
rs7207889	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7209094	0.81[EUR][1000 genomes]
rs7210655	0.81[EUR][1000 genomes]
rs7214891	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7216834	0.80[EUR][1000 genomes]
rs7217614	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7223346	0.84[EUR][1000 genomes]
rs72833498	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs758853	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8064702	0.83[EUR][1000 genomes]
rs8065190	0.85[EUR][1000 genomes]
rs8075345	0.80[EUR][1000 genomes]
rs8076669	0.83[EUR][1000 genomes]
rs8076864	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080221	0.82[EUR][1000 genomes]
rs8080706	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8081406	0.84[EUR][1000 genomes]
rs8081667	0.81[EUR][1000 genomes]
rs9652827	0.85[EUR][1000 genomes]
rs9652828	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9709250	0.85[EUR][1000 genomes]
rs9889745	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9889822	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9890012	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9891379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9891646	0.81[EUR][1000 genomes]
rs9891938	0.80[EUR][1000 genomes]
rs9896441	0.85[EUR][1000 genomes]
rs9897542	0.82[EUR][1000 genomes]
rs9898313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899002	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9902141	0.81[EUR][1000 genomes]
rs9905429	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907313	0.80[EUR][1000 genomes]
rs9908031	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909615	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9909697	0.84[EUR][1000 genomes]
rs9916868	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
5	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv907706	chr17:15731923-16056442	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv1067555	chr17:15804228-16001117	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
9	nsv1062220	chr17:15869557-16093156	Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv1064878	chr17:15869557-16097241	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1055173	chr17:15875935-16097241	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv1056157	chr17:15890584-16088473	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
13	nsv833377	chr17:15912013-16104515	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv522169	chr17:15923709-16147821	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
15	esv1792054	chr17:15934025-16010920	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12942295	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs12942295	ADORA2B	cis	Nerve Tibial	GTEx
rs12942295	ADORA2B	cis	Esophagus Muscularis	GTEx
rs12942295	CENPV	cis	Artery Tibial	GTEx
rs12942295	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs12942295	ZSWIM7	cis	Muscle Skeletal	GTEx
rs12942295	ADORA2B	cis	Thyroid	GTEx
rs12942295	ADORA2B	cis	Muscle Skeletal	GTEx
rs12942295	ADORA2B	cis	Artery Tibial	GTEx
rs12942295	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs12942295	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15905200-15986400	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr17:15913800-15990800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr17:15915400-15998000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr17:15921000-15991000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr17:15921000-15991200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr17:15923800-15998000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:15926800-15985400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:15926800-15987600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr17:15927200-15976400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr17:15927800-15987800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:15931800-15988800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:15940000-15980600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:15942000-15985000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:15944800-15991000	Strong transcription	Fetal Intestine Large	intestine
15	chr17:15948200-15975200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:15948200-15978800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:15953800-15988400	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr17:15954000-15986000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr17:15954200-15974600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:15954200-15985400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr17:15955800-15975600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr17:15955800-15976000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr17:15955800-15982200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:15955800-15985400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr17:15955800-15985400	Strong transcription	Primary B cells from cord blood	blood
26	chr17:15955800-15985600	Strong transcription	Dnd41	blood
27	chr17:15955800-15990600	Strong transcription	Fetal Thymus	thymus
28	chr17:15956200-15985400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr17:15956400-15984000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:15956400-15985600	Strong transcription	Adipose Nuclei	Adipose
31	chr17:15956400-15990800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr17:15956800-15979600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr17:15957000-15985400	Strong transcription	Liver	Liver
34	chr17:15957400-15988200	Strong transcription	Primary T cells from cord blood	blood
35	chr17:15957400-15990600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr17:15957600-15975000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr17:15957600-15979200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr17:15957600-15980600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr17:15957600-15986400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:15957600-15988400	Strong transcription	A549	lung
41	chr17:15958000-15984000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:15958000-15991000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:15958200-15988000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:15958400-15985000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:15958400-15985600	Strong transcription	GM12878-XiMat	blood
46	chr17:15958800-15975000	Strong transcription	Fetal Muscle Leg	muscle
47	chr17:15958800-15985800	Strong transcription	Osteobl	bone
48	chr17:15959000-15975600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr17:15959000-15975600	Strong transcription	NHDF-Ad	bronchial
50	chr17:15959200-15981400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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