Variant report

Variant	rs28431824
Chromosome Location	chr17:16553528-16553529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16535365..16539070-chr17:16551743..16556153,5	MCF-7	breast:
2	chr17:16437964..16442048-chr17:16550999..16555622,7	MCF-7	breast:
3	chr17:16551114..16553822-chr17:16554549..16558293,3	K562	blood:

Variant related genes	Relation type
ENSG00000264765	Chromatin interaction
ENSG00000197566	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1005369	0.98[ASN][1000 genomes]
rs1005370	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12051673	0.94[ASN][1000 genomes]
rs12051751	0.86[EUR][1000 genomes]
rs12103873	0.85[ASN][1000 genomes]
rs16959857	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16959869	0.98[ASN][1000 genomes]
rs16959870	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28458310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458353	1.00[ASN][1000 genomes]
rs28525101	0.82[ASN][1000 genomes]
rs28525658	0.96[ASN][1000 genomes]
rs28526077	0.90[ASN][1000 genomes]
rs28612609	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28626982	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636605	0.96[ASN][1000 genomes]
rs28674185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28751872	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754336	1.00[ASN][1000 genomes]
rs28792801	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28826699	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28865976	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28875211	0.98[ASN][1000 genomes]
rs3813762	0.98[ASN][1000 genomes]
rs4239135	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4352086	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791672	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4791673	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4791676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791678	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792757	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792761	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5000166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55920274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56303920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57305125	0.94[EUR][1000 genomes]
rs57448521	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57694811	0.94[EUR][1000 genomes]
rs58164310	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59486407	1.00[ASN][1000 genomes]
rs59594997	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59826203	0.98[ASN][1000 genomes]
rs62072781	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62072790	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62072792	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62072845	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62073660	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6502514	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7208075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213274	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217544	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7217717	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7218241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219632	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7221518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222622	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7222875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225641	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226328	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72637355	0.93[ASN][1000 genomes]
rs72637356	0.98[ASN][1000 genomes]
rs72637357	0.98[ASN][1000 genomes]
rs72637358	0.98[ASN][1000 genomes]
rs72637359	1.00[ASN][1000 genomes]
rs72637360	1.00[ASN][1000 genomes]
rs72637361	0.85[ASN][1000 genomes]
rs72637362	0.88[ASN][1000 genomes]
rs72637363	0.84[ASN][1000 genomes]
rs8065558	0.98[ASN][1000 genomes]
rs8068349	1.00[ASN][1000 genomes]
rs8069286	0.94[EUR][1000 genomes]
rs8074285	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074464	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074487	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075988	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8076849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8082225	0.96[ASN][1000 genomes]
rs8082323	0.94[EUR][1000 genomes]
rs8082462	0.94[EUR][1000 genomes]
rs8082650	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889227	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9890123	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9890698	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9891138	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9892170	0.83[EUR][1000 genomes]
rs9894637	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9898888	0.88[ASN][1000 genomes]
rs9899785	1.00[ASN][1000 genomes]
rs9899919	0.99[ASN][1000 genomes]
rs9901145	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9904901	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9905710	0.98[ASN][1000 genomes]
rs9906261	0.98[ASN][1000 genomes]
rs9906728	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9907785	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9908015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908390	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909044	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9909955	0.98[ASN][1000 genomes]
rs9910087	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9910842	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911162	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911524	1.00[ASN][1000 genomes]
rs9911608	1.00[ASN][1000 genomes]
rs9911677	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9911820	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911851	0.98[ASN][1000 genomes]
rs9915121	0.85[ASN][1000 genomes]
rs9916069	1.00[ASN][1000 genomes]
rs9916258	1.00[ASN][1000 genomes]
rs9916819	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
4	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv2758442	chr17:16527056-16817437	Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv2758676	chr17:16527056-16817437	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv427991	chr17:16527056-16817437	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16527800-16556000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:16528000-16556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:16530000-16555400	Weak transcription	Small Intestine	intestine
4	chr17:16531200-16556200	Weak transcription	Right Ventricle	heart
5	chr17:16531800-16556000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:16532200-16556000	Weak transcription	NHLF	lung
7	chr17:16532400-16556600	Weak transcription	Lung	lung
8	chr17:16533400-16556000	Weak transcription	HUVEC	blood vessel
9	chr17:16533400-16556400	Weak transcription	Aorta	Aorta
10	chr17:16535000-16556000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:16535000-16556000	Weak transcription	Spleen	Spleen
12	chr17:16535600-16556000	Weak transcription	Pancreas	Pancrea
13	chr17:16535800-16555400	Weak transcription	NHEK	skin
14	chr17:16536400-16556000	Weak transcription	Esophagus	oesophagus
15	chr17:16536600-16556000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr17:16537200-16556000	Weak transcription	Fetal Stomach	stomach
17	chr17:16537400-16555600	Weak transcription	Fetal Brain Female	brain
18	chr17:16537400-16556000	Weak transcription	HMEC	breast
19	chr17:16537600-16555400	Weak transcription	Fetal Brain Male	brain
20	chr17:16537800-16556000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr17:16537800-16556000	Weak transcription	Fetal Thymus	thymus
22	chr17:16538000-16555400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr17:16538000-16555400	Weak transcription	Brain Anterior Caudate	brain
24	chr17:16538000-16555400	Weak transcription	Brain Substantia Nigra	brain
25	chr17:16538000-16555400	Weak transcription	Psoas Muscle	Psoas
26	chr17:16538000-16556000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr17:16538000-16556000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr17:16538000-16556000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr17:16538000-16556000	Weak transcription	Thymus	Thymus
30	chr17:16538000-16556000	Weak transcription	NH-A	brain
31	chr17:16538000-16556000	Weak transcription	Osteobl	bone
32	chr17:16538000-16556400	Weak transcription	Left Ventricle	heart
33	chr17:16538200-16555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:16538200-16555400	Weak transcription	Fetal Kidney	kidney
35	chr17:16538200-16555400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:16538200-16555600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr17:16538200-16556000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr17:16538200-16556000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr17:16538200-16556000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr17:16538200-16556000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr17:16538200-16556000	Weak transcription	Brain Hippocampus Middle	brain
42	chr17:16538200-16556000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr17:16538200-16556000	Weak transcription	Ovary	ovary
44	chr17:16538200-16556000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr17:16538200-16556000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr17:16538200-16556000	Weak transcription	HSMMtube	muscle
47	chr17:16538400-16555400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr17:16539400-16556000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:16543000-16556000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:16543200-16556000	Weak transcription	HepG2	liver

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