Variant report

Variant	rs178839
Chromosome Location	chr17:16073871-16073872
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16073671..16077871-chr17:16116736..16119410,7	MCF-7	breast:
2	chr17:16072733..16074732-chr17:16076435..16078700,2	MCF-7	breast:
3	chr17:16073606..16076574-chr17:16118247..16120387,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10451230	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1045599	0.85[CEU][hapmap]
rs1065822	0.86[CEU][hapmap]
rs1075901	0.96[CEU][hapmap]
rs1079533	0.85[CEU][hapmap]
rs1125156	0.86[CEU][hapmap]
rs1160109	0.83[CEU][hapmap]
rs11650678	0.83[CEU][hapmap]
rs11651290	0.85[CEU][hapmap]
rs11654	0.86[CEU][hapmap]
rs11657160	1.00[CEU][hapmap]
rs11658564	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11869450	0.96[CEU][hapmap]
rs11869563	0.96[CEU][hapmap]
rs11870608	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11872032	0.83[CEU][hapmap]
rs12946619	0.82[CEU][hapmap]
rs178653	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs178654	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs178657	0.85[CEU][hapmap]
rs178787	0.85[CEU][hapmap]
rs178789	0.89[CEU][hapmap]
rs178791	0.89[CEU][hapmap]
rs178797	0.89[CEU][hapmap]
rs178798	0.85[CEU][hapmap]
rs178799	0.83[CEU][hapmap]
rs178802	0.82[CEU][hapmap]
rs178805	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs178807	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178809	0.83[CEU][hapmap]
rs178810	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs178814	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs178815	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs178816	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs178817	0.81[EUR][1000 genomes]
rs178818	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs178820	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs178821	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178822	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178824	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178825	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178826	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178827	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178828	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178829	0.83[EUR][1000 genomes]
rs178830	0.81[EUR][1000 genomes]
rs178831	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs178833	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178834	0.83[EUR][1000 genomes]
rs178835	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178836	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs178837	0.81[EUR][1000 genomes]
rs178838	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1989856	0.85[CEU][hapmap]
rs2041460	0.81[CEU][hapmap]
rs2078050	1.00[CEU][hapmap]
rs21180	0.81[EUR][1000 genomes]
rs2157990	0.96[CEU][hapmap]
rs2157991	1.00[CEU][hapmap]
rs2157992	0.85[CEU][hapmap]
rs2285579	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2285580	0.83[EUR][1000 genomes]
rs2286795	0.89[CEU][hapmap]
rs2286796	0.86[CEU][hapmap]
rs2301652	0.82[CEU][hapmap]
rs2302415	0.96[CEU][hapmap]
rs2324141	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2324142	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2779212	0.85[CEU][hapmap]
rs2875265	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35375077	0.83[AMR][1000 genomes]
rs3760293	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3760298	0.82[CEU][hapmap]
rs3785628	1.00[CEU][hapmap]
rs3785631	0.85[CEU][hapmap]
rs3785632	0.82[CEU][hapmap]
rs3785633	0.85[CEU][hapmap]
rs3815039	0.85[CEU][hapmap]
rs3826360	0.85[CEU][hapmap]
rs4435297	0.96[CEU][hapmap]
rs4566208	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4791662	0.83[CEU][hapmap]
rs4792715	0.96[CEU][hapmap]
rs4792717	1.00[CEU][hapmap]
rs4792718	0.96[CEU][hapmap]
rs4792721	0.85[CEU][hapmap]
rs545738	0.82[EUR][1000 genomes]
rs55844265	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6416868	0.96[CEU][hapmap]
rs6502482	1.00[CEU][hapmap]
rs6502488	1.00[CEU][hapmap]
rs6502491	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7207463	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7214695	1.00[CEU][hapmap]
rs7222886	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7223346	1.00[CEU][hapmap]
rs758853	0.82[CEU][hapmap]
rs8064702	0.86[AMR][1000 genomes]
rs8070859	0.96[CEU][hapmap]
rs8076864	0.89[CEU][hapmap]
rs8079969	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9890012	0.85[CEU][hapmap]
rs9891379	0.85[CEU][hapmap]
rs9891938	0.96[CEU][hapmap]
rs9897388	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9899002	0.86[CEU][hapmap]
rs9902141	0.85[CEU][hapmap]
rs9905225	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9907273	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9908031	0.89[CEU][hapmap]
rs9908591	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9909697	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
6	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
7	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
8	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
9	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
10	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
11	nsv907711	chr17:15978663-16092902	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv907712	chr17:15981874-16103426	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv962265	chr17:16064412-16074713	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs178839	LOC125150	cis	uninvolved skin	skin_eQTL
rs178839	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs178839	ZSWIM7	cis	Muscle Skeletal	GTEx
rs178839	ADORA2B	cis	lung	GTEx
rs178839	ADORA2B	cis	Artery Tibial	GTEx
rs178839	ADORA2B	cis	Thyroid	GTEx
rs178839	Hs.379903	cis	multi-tissue	Pritchard
rs178839	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs178839	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs178839	CENPV	cis	Artery Tibial	GTEx
rs178839	ADORA2B	cis	Esophagus Muscularis	GTEx
rs178839	ADORA2B	cis	Muscle Skeletal	GTEx
rs178839	LOC125150	cis	lesional skin	skin_eQTL
rs178839	ADORA2B	cis	Nerve Tibial	GTEx
rs178839	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs178839	LOC125150	cis	normal skin	skin_eQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16015600-16077600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr17:16021800-16087600	Weak transcription	Fetal Brain Male	brain
3	chr17:16035800-16103400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr17:16039200-16096800	Weak transcription	K562	blood
5	chr17:16042000-16094200	Weak transcription	Psoas Muscle	Psoas
6	chr17:16048400-16088000	Weak transcription	Fetal Brain Female	brain
7	chr17:16049200-16077600	Weak transcription	Right Ventricle	heart
8	chr17:16049200-16088600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:16049200-16093200	Weak transcription	Aorta	Aorta
10	chr17:16049200-16103400	Weak transcription	Spleen	Spleen
11	chr17:16049200-16108600	Weak transcription	Esophagus	oesophagus
12	chr17:16051800-16089400	Weak transcription	Brain Germinal Matrix	brain
13	chr17:16052000-16089000	Weak transcription	HSMMtube	muscle
14	chr17:16052200-16100400	Weak transcription	Ovary	ovary
15	chr17:16053200-16074800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:16055000-16075800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:16055000-16088600	Weak transcription	Colonic Mucosa	Colon
18	chr17:16055200-16075000	Weak transcription	HMEC	breast
19	chr17:16055200-16089400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr17:16055200-16102600	Weak transcription	Brain Angular Gyrus	brain
21	chr17:16055400-16094000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr17:16055400-16104000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr17:16055800-16102000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr17:16056200-16083800	Weak transcription	Gastric	stomach
25	chr17:16057200-16074200	Weak transcription	Hela-S3	cervix
26	chr17:16058000-16074200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr17:16058400-16074800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr17:16059400-16075000	Weak transcription	Thymus	Thymus
29	chr17:16059400-16083400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:16059400-16094200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr17:16059400-16102400	Weak transcription	Small Intestine	intestine
32	chr17:16059400-16102400	Weak transcription	NHLF	lung
33	chr17:16059400-16102800	Weak transcription	Pancreas	Pancrea
34	chr17:16059800-16093200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:16060000-16083600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr17:16060600-16087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr17:16061200-16089200	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:16061400-16075000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr17:16061400-16087200	Weak transcription	Fetal Kidney	kidney
40	chr17:16061600-16074800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:16062200-16074400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr17:16062200-16074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:16062200-16093200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr17:16062400-16074200	Weak transcription	Placenta	Placenta
45	chr17:16062400-16074200	Weak transcription	HUVEC	blood vessel
46	chr17:16062400-16074400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:16062400-16074600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:16062600-16074000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr17:16062600-16075000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr17:16063000-16074600	Weak transcription	NHDF-Ad	bronchial

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