Variant report

Variant	rs178801
Chromosome Location	chr17:16108464-16108465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16108186..16110773-chr17:16115629..16120771,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141027	Chromatin interaction
ENSG00000108474	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10852833	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11078332	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1125156	0.87[AMR][1000 genomes]
rs1126148	0.84[AMR][1000 genomes]
rs1160109	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11650678	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11655773	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11871961	0.84[AMR][1000 genomes]
rs12150017	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12449895	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12939418	0.90[AMR][1000 genomes]
rs12947205	0.81[AMR][1000 genomes]
rs178657	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs178658	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs178659	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs178662	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178789	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178790	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs178791	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178792	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178793	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178794	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs178795	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs178796	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs178797	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs178798	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs178799	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs178800	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178802	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs178803	0.81[ASN][1000 genomes]
rs178804	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs178805	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs178806	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs178808	0.87[EUR][1000 genomes]
rs178809	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178816	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178817	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178820	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178829	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs178830	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs178834	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs178837	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1972503	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1989856	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2051736	0.85[AMR][1000 genomes]
rs21180	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34243080	0.83[AMR][1000 genomes]
rs34351630	0.81[AMR][1000 genomes]
rs35160872	0.82[AMR][1000 genomes]
rs35799415	0.86[AMR][1000 genomes]
rs36001065	0.81[AMR][1000 genomes]
rs4791661	0.86[AMR][1000 genomes]
rs545738	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7216834	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72833498	0.87[AMR][1000 genomes]
rs8080706	0.80[AMR][1000 genomes]
rs9891646	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9902141	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9903464	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9907313	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9909697	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	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
4	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
5	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
6	nsv907713	chr17:15981874-16127206	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv907714	chr17:15990013-16110384	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
9	nsv907716	chr17:16068422-16116835	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
11	nsv907718	chr17:16080849-16143709	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
12	nsv960423	chr17:16089865-16112673	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv528263	chr17:16097430-16196996	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs178801	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs178801	ADORA2B	cis	Muscle Skeletal	GTEx
rs178801	ADORA2B	cis	Artery Tibial	GTEx
rs178801	ZSWIM7	cis	Muscle Skeletal	GTEx
rs178801	CENPV	cis	Artery Tibial	GTEx
rs178801	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs178801	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs178801	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs178801	ADORA2B	cis	Esophagus Muscularis	GTEx
rs178801	ADORA2B	cis	Nerve Tibial	GTEx
rs178801	ADORA2B	cis	Thyroid	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16049200-16108600	Weak transcription	Esophagus	oesophagus
2	chr17:16088000-16117000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:16088200-16116200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:16089600-16114600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr17:16090000-16116800	Weak transcription	NH-A	brain
6	chr17:16093600-16117000	Weak transcription	Aorta	Aorta
7	chr17:16095200-16117000	Weak transcription	Right Ventricle	heart
8	chr17:16101200-16114800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:16101600-16116000	Weak transcription	Thymus	Thymus
10	chr17:16101800-16111000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr17:16101800-16117000	Weak transcription	Fetal Stomach	stomach
12	chr17:16102200-16110200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr17:16102400-16116800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr17:16102800-16111800	Weak transcription	K562	blood
15	chr17:16103200-16111800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:16104000-16117000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr17:16104200-16114600	Weak transcription	Primary B cells from cord blood	blood
18	chr17:16105200-16108800	Weak transcription	NHDF-Ad	bronchial
19	chr17:16105200-16116000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr17:16105200-16117000	Weak transcription	NHEK	skin
21	chr17:16105400-16116200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr17:16105400-16118000	Weak transcription	Spleen	Spleen
23	chr17:16106000-16108800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:16106400-16114200	Weak transcription	Psoas Muscle	Psoas
25	chr17:16106400-16116800	Weak transcription	NHLF	lung
26	chr17:16106400-16117000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:16106800-16108600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:16106800-16109800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr17:16106800-16110000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr17:16106800-16110600	Weak transcription	Colonic Mucosa	Colon
31	chr17:16106800-16111800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr17:16106800-16112200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:16106800-16114600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:16106800-16114600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr17:16106800-16114600	Weak transcription	Ovary	ovary
36	chr17:16106800-16115000	Weak transcription	Adipose Nuclei	Adipose
37	chr17:16106800-16115000	Weak transcription	Hela-S3	cervix
38	chr17:16106800-16115400	Weak transcription	Left Ventricle	heart
39	chr17:16106800-16116000	Weak transcription	Right Atrium	heart
40	chr17:16106800-16116800	Weak transcription	Fetal Lung	lung
41	chr17:16106800-16118000	Weak transcription	Lung	lung
42	chr17:16107000-16110000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:16107000-16114200	Weak transcription	HepG2	liver
44	chr17:16107000-16114600	Weak transcription	Primary T cells from cord blood	blood
45	chr17:16107000-16115400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr17:16107000-16115600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr17:16107000-16116000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr17:16107000-16116800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr17:16107000-16117000	Weak transcription	Brain Anterior Caudate	brain
50	chr17:16107000-16117000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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