Variant report

Variant	rs178789
Chromosome Location	chr17:16131196-16131197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16118757..16122338-chr17:16126613..16132237,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108474	Chromatin interaction
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1029809	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1065822	0.96[CEU][hapmap]
rs1075901	0.88[CEU][hapmap]
rs1079533	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.80[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap]
rs10852833	0.87[AMR][1000 genomes]
rs11078332	0.81[AMR][1000 genomes]
rs1125156	0.96[CEU][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes]
rs1160109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs11650427	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs11650678	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs11651290	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.80[LWK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs11651578	0.92[YRI][hapmap]
rs11653650	0.80[EUR][1000 genomes]
rs11655773	0.83[AMR][1000 genomes]
rs11656811	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs11657160	0.89[CEU][hapmap]
rs11868284	0.85[YRI][hapmap]
rs11872032	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12150017	0.81[AMR][1000 genomes]
rs12936233	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs12939418	0.85[AMR][1000 genomes]
rs12945855	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs178657	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes]
rs178658	0.91[AMR][1000 genomes]
rs178659	0.85[AMR][1000 genomes]
rs178662	0.83[AMR][1000 genomes]
rs178790	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178792	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178793	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178794	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs178795	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs178796	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs178797	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178798	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178799	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs178800	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs178801	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178802	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178804	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs178805	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178809	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs178814	0.89[CEU][hapmap]
rs178815	0.89[CEU][hapmap]
rs178816	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs178817	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178820	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178822	0.89[CEU][hapmap]
rs178829	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178830	0.84[AMR][1000 genomes]
rs178834	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs178837	0.91[ASW][hapmap];0.89[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes]
rs178838	0.88[CEU][hapmap]
rs178839	0.89[CEU][hapmap]
rs1972503	0.85[AMR][1000 genomes]
rs1989856	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs2078050	0.89[CEU][hapmap]
rs21180	0.83[AMR][1000 genomes]
rs2157990	0.85[CEU][hapmap]
rs2157991	0.89[CEU][hapmap]
rs2324141	0.89[CEU][hapmap]
rs2324142	0.89[CEU][hapmap]
rs35799415	0.81[AMR][1000 genomes]
rs3785625	0.92[YRI][hapmap]
rs3785628	0.89[CEU][hapmap]
rs3785631	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs3815039	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.80[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap]
rs4435297	0.89[CEU][hapmap]
rs4791661	0.81[AMR][1000 genomes]
rs4791662	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4792717	0.89[CEU][hapmap]
rs4792718	0.85[CEU][hapmap]
rs4792721	0.81[TSI][hapmap]
rs545738	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62072528	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6502488	0.89[CEU][hapmap]
rs7214695	0.89[CEU][hapmap]
rs7215071	0.86[AFR][1000 genomes]
rs7216834	0.85[AMR][1000 genomes]
rs7223346	0.89[CEU][hapmap]
rs72833498	0.82[AMR][1000 genomes]
rs8076864	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.80[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap]
rs8079969	0.89[CEU][hapmap]
rs9890012	0.96[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs9891379	0.96[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap]
rs9891646	0.85[AMR][1000 genomes]
rs9902141	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes]
rs9903464	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes]
rs9907313	0.85[AMR][1000 genomes]
rs9908031	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs9909022	0.83[AFR][1000 genomes]
rs9909697	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs9916220	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
7	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
8	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
9	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs178789	ADORA2B	cis	Nerve Tibial	GTEx
rs178789	TTC19	cis	lymphoblastoid	seeQTL
rs178789	ADORA2B	cis	Thyroid	GTEx
rs178789	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs178789	ADORA2B	cis	Esophagus Muscularis	GTEx
rs178789	ADORA2B	cis	Artery Tibial	GTEx
rs178789	ADORA2B	cis	Muscle Skeletal	GTEx
rs178789	CENPV	cis	Artery Tibial	GTEx
rs178789	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs178789	ZSWIM7	cis	Muscle Skeletal	GTEx
rs178789	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs178789	TTC19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16121000-16163200	Weak transcription	Spleen	Spleen
2	chr17:16121200-16141400	Weak transcription	Brain Substantia Nigra	brain
3	chr17:16121200-16142800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:16121200-16157000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:16121200-16158800	Weak transcription	Left Ventricle	heart
6	chr17:16121200-16159800	Weak transcription	Lung	lung
7	chr17:16121200-16163000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:16121400-16132200	Weak transcription	HSMM	muscle
9	chr17:16121400-16132200	Weak transcription	NHLF	lung
10	chr17:16121400-16133000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr17:16121400-16133200	Weak transcription	Fetal Thymus	thymus
12	chr17:16121400-16137400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:16121400-16140200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr17:16121400-16140400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:16121400-16141400	Weak transcription	Colon Smooth Muscle	Colon
16	chr17:16121400-16158600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr17:16121400-16158800	Weak transcription	Fetal Muscle Leg	muscle
18	chr17:16121400-16159000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr17:16121400-16170600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:16121600-16132000	Weak transcription	NHDF-Ad	bronchial
21	chr17:16121600-16132800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr17:16121600-16137000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr17:16121600-16137600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr17:16121600-16139200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr17:16121600-16139400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr17:16121600-16143000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:16121600-16143000	Weak transcription	Fetal Lung	lung
28	chr17:16121600-16147000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:16121600-16150200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr17:16121600-16151800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr17:16121600-16158400	Weak transcription	Brain Hippocampus Middle	brain
32	chr17:16121600-16158600	Weak transcription	Brain Germinal Matrix	brain
33	chr17:16121800-16132000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:16121800-16132600	Weak transcription	HUVEC	blood vessel
35	chr17:16121800-16132800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr17:16121800-16132800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr17:16121800-16132800	Weak transcription	NH-A	brain
38	chr17:16121800-16132800	Weak transcription	Osteobl	bone
39	chr17:16121800-16134000	Weak transcription	Fetal Intestine Large	intestine
40	chr17:16121800-16134200	Weak transcription	Fetal Kidney	kidney
41	chr17:16121800-16137000	Weak transcription	HMEC	breast
42	chr17:16121800-16139000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:16121800-16139200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:16121800-16146600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr17:16121800-16150200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr17:16121800-16153600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr17:16121800-16158200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:16121800-16158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr17:16121800-16163200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr17:16121800-16163200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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