Variant report

Variant	rs7206589
Chromosome Location	chr16:75446257-75446258
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75445412..75447082-chr16:75465905..75468700,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10438605	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11149817	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12149472	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149940	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444789	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445803	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716785	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12918234	0.86[ASN][1000 genomes]
rs12919055	0.89[ASN][1000 genomes]
rs12921808	1.00[ASN][1000 genomes]
rs12926447	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928461	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12935491	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337069	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13339257	0.96[ASN][1000 genomes]
rs17605695	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17674216	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285221	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2550325	1.00[ASN][1000 genomes]
rs2550916	1.00[ASN][1000 genomes]
rs2650408	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650409	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28368934	0.90[ASN][1000 genomes]
rs28371085	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28510780	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28525459	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34532060	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4081763	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383172	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55715607	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719515	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59800961	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60544814	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6625	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71380715	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7184596	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7185880	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7186825	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7188111	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7189037	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7206780	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs729109	0.93[ASN][1000 genomes]
rs8046261	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047147	0.85[ASN][1000 genomes]
rs8047983	0.93[ASN][1000 genomes]
rs8048683	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050367	0.89[ASN][1000 genomes]
rs8051151	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051238	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052405	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052555	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054557	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8055098	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8056345	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056473	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057652	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8057925	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8059427	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8059883	0.93[ASN][1000 genomes]
rs8060338	0.93[ASN][1000 genomes]
rs8063733	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9319483	1.00[ASN][1000 genomes]
rs9319484	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9745455	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921115	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921330	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923034	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923465	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9923574	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924524	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926453	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9926933	0.93[ASN][1000 genomes]
rs9927330	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928744	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928901	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930002	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9932982	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935954	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935967	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936641	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936648	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936853	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9937903	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9938936	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939080	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939587	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9940189	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940884	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941142	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972714	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	esv2422358	chr16:75381762-75456763	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
6	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv1062023	chr16:75427013-75461626	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7206589	RP11-252K23.2	cis	Esophagus Muscularis	GTEx
rs7206589	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs7206589	RP11-252K23.2	cis	Nerve Tibial	GTEx
rs7206589	RP11-252K23.2	cis	Artery Tibial	GTEx
rs7206589	RP11-252K23.2	cis	Thyroid	GTEx
rs7206589	RP11-252K23.2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75406000-75453400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:75407200-75454200	Weak transcription	Stomach Mucosa	stomach
3	chr16:75415600-75453400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr16:75425400-75454200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr16:75425400-75457200	Weak transcription	Fetal Brain Male	brain
6	chr16:75427200-75449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:75427200-75464400	Weak transcription	Esophagus	oesophagus
8	chr16:75427200-75465400	Weak transcription	Spleen	Spleen
9	chr16:75428200-75453400	Weak transcription	Psoas Muscle	Psoas
10	chr16:75429000-75454400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr16:75429000-75454800	Weak transcription	HMEC	breast
12	chr16:75429200-75453400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr16:75429200-75454800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr16:75429200-75455000	Weak transcription	Gastric	stomach
15	chr16:75432400-75465400	Weak transcription	Pancreas	Pancrea
16	chr16:75432400-75466600	Weak transcription	Aorta	Aorta
17	chr16:75432600-75446400	Weak transcription	Right Atrium	heart
18	chr16:75437000-75447600	Strong transcription	Fetal Intestine Small	intestine
19	chr16:75437200-75448400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr16:75437200-75454200	Weak transcription	Fetal Heart	heart
21	chr16:75438200-75446600	Strong transcription	Fetal Intestine Large	intestine
22	chr16:75438400-75446800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr16:75438400-75446800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr16:75438400-75448200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:75438400-75448600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr16:75438400-75448800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr16:75438600-75446800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr16:75438600-75447200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr16:75438600-75448600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr16:75438600-75448600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr16:75438800-75446800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr16:75438800-75447200	Strong transcription	Fetal Thymus	thymus
33	chr16:75439000-75448600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:75439200-75447400	Strong transcription	Fetal Muscle Leg	muscle
35	chr16:75439200-75447400	Strong transcription	Fetal Stomach	stomach
36	chr16:75439400-75446800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr16:75439600-75447400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr16:75439600-75447400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr16:75439800-75446400	Strong transcription	Adipose Nuclei	Adipose
40	chr16:75439800-75447800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr16:75440000-75446800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr16:75440000-75447000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr16:75440000-75447200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr16:75440400-75447400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr16:75440600-75448600	Strong transcription	Primary T cells from cord blood	blood
46	chr16:75440600-75448600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr16:75440800-75446800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:75441000-75446800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr16:75441400-75446800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr16:75441600-75447400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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