Variant report

Variant	rs71623
Chromosome Location	chr20:52661095-52661096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:56707748..56711068-chr20:52660176..52663748,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11699406	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs158539	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158541	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158546	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158549	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158550	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs208642	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs208644	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2299720	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290384	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290386	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290388	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290390	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290417	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290421	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290453	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290456	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290457	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290458	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290459	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290462	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290466	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290471	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
3	esv2763673	chr20:52637074-52668126	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv3419	chr20:52637581-52672115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
5	nsv1065821	chr20:52644856-52662562	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv912940	chr20:52646029-52663409	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv912942	chr20:52646926-52663409	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv1059343	chr20:52647808-52662562	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	nsv1065004	chr20:52647808-52665631	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv2760671	chr20:52647808-52665643	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv1055891	chr20:52647808-52666885	Enhancers Strong transcription Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
12	nsv1067336	chr20:52647808-52668126	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	nsv1065888	chr20:52647808-52670378	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv586247	chr20:52647823-52663409	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
15	nsv433324	chr20:52647823-52663783	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
16	nsv586248	chr20:52647823-52663783	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
17	nsv586249	chr20:52647823-52664869	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
18	nsv586250	chr20:52647823-52671132	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
19	nsv586260	chr20:52647830-52663783	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
20	nsv586261	chr20:52647830-52664869	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
21	nsv586268	chr20:52648368-52663409	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
22	nsv1066172	chr20:52651154-52662562	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
23	nsv1055306	chr20:52651154-52666885	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
24	nsv1063512	chr20:52651609-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
25	nsv1067083	chr20:52651609-52665631	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
26	nsv179659	chr20:52651946-52661376	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
27	nsv1065957	chr20:52651963-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
28	nsv1060202	chr20:52652050-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
29	nsv1061631	chr20:52652346-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
30	nsv1062635	chr20:52652471-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
2	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:52657800-52664800	Weak transcription	HSMMtube	muscle
6	chr20:52659600-52661800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr20:52660000-52661200	Enhancers	Osteobl	bone
8	chr20:52660200-52661600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr20:52660200-52661600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr20:52660400-52664200	Weak transcription	Right Atrium	heart
11	chr20:52660800-52661600	Enhancers	K562	blood
12	chr20:52661000-52661400	Weak transcription	NHDF-Ad	bronchial
13	chr20:52661000-52661400	Weak transcription	NHLF	lung

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