Variant report

Variant	rs28558522
Chromosome Location	chr14:45419237-45419238
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:45417495..45420324-chr14:45602844..45604694,2	MCF-7	breast:
2	chr14:45417653..45420014-chr14:45428593..45430764,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100442	Chromatin interaction
ENSG00000179454	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10083439	0.87[EUR][1000 genomes]
rs10129173	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10131066	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10131615	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10132389	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10132547	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10132949	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10134071	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10134598	0.81[EUR][1000 genomes]
rs10135085	0.82[AMR][1000 genomes]
rs10135890	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10136008	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10136855	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10136926	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10137510	0.82[AFR][1000 genomes]
rs10138272	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10139998	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10140013	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140049	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10140108	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10140222	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10140318	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10145092	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10145267	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10146395	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10147499	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10149484	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10150646	0.87[EUR][1000 genomes]
rs10152101	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1053667	0.92[EUR][1000 genomes]
rs11157423	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11157424	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11844832	0.86[EUR][1000 genomes]
rs11845088	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11845904	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11845956	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11846656	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11847039	0.87[EUR][1000 genomes]
rs11848334	0.98[EUR][1000 genomes]
rs11848799	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11849208	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11849583	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11850363	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11851218	0.87[EUR][1000 genomes]
rs11851357	0.87[EUR][1000 genomes]
rs11851516	0.87[EUR][1000 genomes]
rs11851962	0.98[EUR][1000 genomes]
rs11852210	0.98[EUR][1000 genomes]
rs12100842	0.94[EUR][1000 genomes]
rs1593279	0.87[EUR][1000 genomes]
rs17115639	0.87[EUR][1000 genomes]
rs17115646	0.87[EUR][1000 genomes]
rs17115648	0.87[EUR][1000 genomes]
rs17115652	0.87[EUR][1000 genomes]
rs17115677	0.87[EUR][1000 genomes]
rs17115688	0.98[EUR][1000 genomes]
rs17115703	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115718	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17115787	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2295157	0.87[EUR][1000 genomes]
rs28432035	0.87[EUR][1000 genomes]
rs28448551	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28517769	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28572336	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28594810	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28622413	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28681969	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28695721	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703636	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28756151	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899960	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736747	0.85[EUR][1000 genomes]
rs3825629	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4141578	0.95[ASN][1000 genomes]
rs56386358	0.84[EUR][1000 genomes]
rs56706956	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56836063	0.86[EUR][1000 genomes]
rs57129780	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57147026	0.82[EUR][1000 genomes]
rs57614513	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57694277	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58013518	0.98[EUR][1000 genomes]
rs58338525	0.87[EUR][1000 genomes]
rs58920861	0.98[EUR][1000 genomes]
rs59992752	0.87[EUR][1000 genomes]
rs60521816	0.87[EUR][1000 genomes]
rs60595870	0.85[EUR][1000 genomes]
rs60891427	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61707578	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6572290	0.98[EUR][1000 genomes]
rs66488071	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66535982	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66662385	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67643245	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7140739	0.87[EUR][1000 genomes]
rs7145831	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7145870	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7146566	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7147644	0.95[ASN][1000 genomes]
rs7147811	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7151557	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7153451	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7158846	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72621070	0.95[ASN][1000 genomes]
rs73334104	0.98[EUR][1000 genomes]
rs73334112	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73334114	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73334131	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73334135	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334148	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334154	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334157	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334162	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334165	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334172	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334176	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73334913	0.94[EUR][1000 genomes]
rs73346336	0.96[EUR][1000 genomes]
rs73346344	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73346351	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73346360	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348060	0.94[ASN][1000 genomes]
rs73348062	0.91[ASN][1000 genomes]
rs73348065	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348069	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73348075	0.95[ASN][1000 genomes]
rs73348076	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73348079	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73348088	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73348095	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73348285	0.95[ASN][1000 genomes]
rs73348939	0.87[EUR][1000 genomes]
rs73348947	0.87[EUR][1000 genomes]
rs73348950	0.87[EUR][1000 genomes]
rs73348953	0.87[EUR][1000 genomes]
rs73348959	0.87[EUR][1000 genomes]
rs73348966	0.94[EUR][1000 genomes]
rs73348975	0.96[EUR][1000 genomes]
rs73348977	0.92[EUR][1000 genomes]
rs73348981	0.98[EUR][1000 genomes]
rs73348987	0.98[EUR][1000 genomes]
rs73349820	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73350007	0.89[ASN][1000 genomes]
rs73350201	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73352233	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73352238	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73352246	0.95[ASN][1000 genomes]
rs73353644	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73353647	0.81[ASN][1000 genomes]
rs73353650	0.81[ASN][1000 genomes]
rs73353657	0.87[EUR][1000 genomes]
rs7493246	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7493823	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8006685	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8015453	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8018380	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8022008	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8022608	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323106	0.92[ASN][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	nsv869289	chr14:44752382-45447415	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1047886	chr14:45189653-45543182	Strong transcription Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv542079	chr14:45189653-45543182	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv901841	chr14:45198196-45719643	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1053437	chr14:45232269-45424222	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv1795667	chr14:45361680-45721052	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	61 gene(s)	inside rSNPs	diseases
7	esv1794986	chr14:45368685-45650813	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv1042585	chr14:45401506-45497907	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv1045869	chr14:45415597-45487903	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28558522	RP11-398E10.1	cis	Nerve Tibial	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45396200-45428400	Weak transcription	HMEC	breast
2	chr14:45402000-45430000	Weak transcription	Colonic Mucosa	Colon
3	chr14:45407800-45428600	Weak transcription	K562	blood
4	chr14:45408400-45429000	Weak transcription	Brain Hippocampus Middle	brain
5	chr14:45408600-45430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:45409400-45429600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr14:45409600-45419600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:45410600-45429200	Weak transcription	Brain Germinal Matrix	brain
9	chr14:45410800-45420400	Weak transcription	Fetal Stomach	stomach
10	chr14:45411800-45421400	Strong transcription	Primary B cells from cord blood	blood
11	chr14:45413200-45428400	Weak transcription	Fetal Brain Female	brain
12	chr14:45413800-45429200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr14:45414800-45427600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr14:45414800-45427600	Weak transcription	HSMMtube	muscle
15	chr14:45414800-45429200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:45415000-45419600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr14:45415000-45420200	Weak transcription	Small Intestine	intestine
18	chr14:45415000-45424600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr14:45415000-45426000	Weak transcription	Pancreas	Pancrea
20	chr14:45415000-45426600	Weak transcription	Brain Angular Gyrus	brain
21	chr14:45415000-45426800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:45415000-45427000	Weak transcription	Fetal Brain Male	brain
23	chr14:45415000-45427400	Weak transcription	A549	lung
24	chr14:45415000-45427600	Weak transcription	Adipose Nuclei	Adipose
25	chr14:45415000-45428400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:45415000-45428600	Weak transcription	Brain Anterior Caudate	brain
27	chr14:45415000-45429400	Weak transcription	Fetal Kidney	kidney
28	chr14:45415000-45429400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr14:45415000-45429600	Weak transcription	Right Ventricle	heart
30	chr14:45415000-45430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr14:45415200-45420200	Weak transcription	Aorta	Aorta
32	chr14:45415200-45420200	Weak transcription	Ovary	ovary
33	chr14:45415200-45420400	Weak transcription	Left Ventricle	heart
34	chr14:45415200-45421600	Weak transcription	Osteobl	bone
35	chr14:45415200-45426200	Weak transcription	Colon Smooth Muscle	Colon
36	chr14:45415200-45426200	Weak transcription	Spleen	Spleen
37	chr14:45415200-45426400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr14:45415200-45426800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr14:45415200-45427400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:45415200-45427400	Weak transcription	Liver	Liver
41	chr14:45415200-45427400	Weak transcription	Fetal Heart	heart
42	chr14:45415200-45428400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr14:45415200-45428400	Weak transcription	HUVEC	blood vessel
44	chr14:45415200-45428400	Weak transcription	NHEK	skin
45	chr14:45415200-45428400	Weak transcription	NHLF	lung
46	chr14:45415200-45428600	Weak transcription	NH-A	brain
47	chr14:45415200-45428800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr14:45415200-45429000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr14:45415200-45429000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr14:45415200-45429200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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