Variant report

Variant	rs178793
Chromosome Location	chr17:16124968-16124969
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16118736..16121992-chr17:16123895..16128426,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108474	Chromatin interaction
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10852833	0.81[AMR][1000 genomes]
rs11078332	0.87[AMR][1000 genomes]
rs1126148	0.85[AMR][1000 genomes]
rs1160109	0.91[AMR][1000 genomes]
rs11650678	0.87[AMR][1000 genomes]
rs11653650	0.84[AFR][1000 genomes]
rs11655773	0.89[AMR][1000 genomes]
rs12150017	0.87[AMR][1000 genomes]
rs12936233	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12945855	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12947205	0.82[AMR][1000 genomes]
rs178657	0.85[AMR][1000 genomes]
rs178658	0.85[AMR][1000 genomes]
rs178659	0.91[AMR][1000 genomes]
rs178662	0.89[AMR][1000 genomes]
rs178789	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178790	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178791	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178792	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178794	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs178795	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178796	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs178797	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178798	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178799	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178800	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs178801	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178802	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178804	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs178805	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178809	0.82[AMR][1000 genomes]
rs178816	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178817	0.84[AMR][1000 genomes]
rs178820	0.87[AMR][1000 genomes]
rs178829	0.87[AMR][1000 genomes]
rs178834	0.93[AMR][1000 genomes]
rs178837	0.80[AMR][1000 genomes]
rs1972503	0.91[AMR][1000 genomes]
rs1989856	0.85[AMR][1000 genomes]
rs35160872	0.83[AMR][1000 genomes]
rs35799415	0.87[AMR][1000 genomes]
rs4791662	0.81[AMR][1000 genomes]
rs545738	0.86[AMR][1000 genomes]
rs7216834	0.91[AMR][1000 genomes]
rs8080706	0.81[AMR][1000 genomes]
rs9891646	0.91[AMR][1000 genomes]
rs9902141	0.85[AMR][1000 genomes]
rs9903464	0.85[AMR][1000 genomes]
rs9907313	0.91[AMR][1000 genomes]
rs9916220	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	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
rs178793	ADORA2B	cis	Esophagus Muscularis	GTEx
rs178793	CENPV	cis	Artery Tibial	GTEx
rs178793	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs178793	ADORA2B	cis	Thyroid	GTEx
rs178793	ADORA2B	cis	Muscle Skeletal	GTEx
rs178793	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs178793	ADORA2B	cis	Nerve Tibial	GTEx
rs178793	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs178793	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs178793	ZSWIM7	cis	Muscle Skeletal	GTEx
rs178793	ADORA2B	cis	Artery Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16121000-16163200	Weak transcription	Spleen	Spleen
2	chr17:16121200-16125000	Weak transcription	Esophagus	oesophagus
3	chr17:16121200-16125200	Weak transcription	Small Intestine	intestine
4	chr17:16121200-16125800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:16121200-16127200	Weak transcription	Placenta	Placenta
6	chr17:16121200-16131000	Weak transcription	Gastric	stomach
7	chr17:16121200-16141400	Weak transcription	Brain Substantia Nigra	brain
8	chr17:16121200-16142800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:16121200-16157000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:16121200-16158800	Weak transcription	Left Ventricle	heart
11	chr17:16121200-16159800	Weak transcription	Lung	lung
12	chr17:16121200-16163000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:16121400-16125200	Weak transcription	Psoas Muscle	Psoas
14	chr17:16121400-16126000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr17:16121400-16128600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr17:16121400-16129600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr17:16121400-16129600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr17:16121400-16129600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:16121400-16130000	Weak transcription	Right Ventricle	heart
20	chr17:16121400-16132200	Weak transcription	HSMM	muscle
21	chr17:16121400-16132200	Weak transcription	NHLF	lung
22	chr17:16121400-16133000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr17:16121400-16133200	Weak transcription	Fetal Thymus	thymus
24	chr17:16121400-16137400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:16121400-16140200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr17:16121400-16140400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr17:16121400-16141400	Weak transcription	Colon Smooth Muscle	Colon
28	chr17:16121400-16158600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr17:16121400-16158800	Weak transcription	Fetal Muscle Leg	muscle
30	chr17:16121400-16159000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr17:16121400-16170600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:16121600-16125600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr17:16121600-16125600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:16121600-16127600	Weak transcription	Brain Angular Gyrus	brain
35	chr17:16121600-16132000	Weak transcription	NHDF-Ad	bronchial
36	chr17:16121600-16132800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr17:16121600-16137000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr17:16121600-16137600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr17:16121600-16139200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr17:16121600-16139400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr17:16121600-16143000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:16121600-16143000	Weak transcription	Fetal Lung	lung
43	chr17:16121600-16147000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr17:16121600-16150200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr17:16121600-16151800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr17:16121600-16158400	Weak transcription	Brain Hippocampus Middle	brain
47	chr17:16121600-16158600	Weak transcription	Brain Germinal Matrix	brain
48	chr17:16121800-16125400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr17:16121800-16125400	Weak transcription	A549	lung
50	chr17:16121800-16125600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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