Variant report

Variant	rs378782
Chromosome Location	chr20:52659458-52659459
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
2	chr20:52557746..52563146-chr20:52657006..52659772,4	MCF-7	breast:
3	chr20:52643210..52646138-chr20:52658422..52660423,2	K562	blood:

Variant related genes	Relation type
ENSG00000064787	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

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];0.97[ASN][1000 genomes]
rs158541	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158546	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158549	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158550	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs208642	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs208644	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs208645	0.95[YRI][hapmap]
rs2299720	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290417	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290421	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290453	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290457	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290458	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290459	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290462	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs290471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71623	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:40 , 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	nsv437187	chr20:52644514-52660120	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	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
7	nsv912939	chr20:52646029-52660741	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv912940	chr20:52646029-52663409	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv517164	chr20:52646926-52660741	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv912941	chr20:52646926-52660741	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv912942	chr20:52646926-52663409	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
12	nsv1059343	chr20:52647808-52662562	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	nsv1065004	chr20:52647808-52665631	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	esv2760671	chr20:52647808-52665643	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
15	nsv1055891	chr20:52647808-52666885	Enhancers Strong transcription Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
16	nsv1067336	chr20:52647808-52668126	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
17	nsv1065888	chr20:52647808-52670378	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
18	nsv586246	chr20:52647823-52660741	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
19	nsv586247	chr20:52647823-52663409	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
20	nsv433324	chr20:52647823-52663783	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
21	nsv586248	chr20:52647823-52663783	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
22	nsv586249	chr20:52647823-52664869	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
23	nsv586250	chr20:52647823-52671132	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
24	nsv586259	chr20:52647830-52660741	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
25	nsv912943	chr20:52647830-52660741	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
26	nsv586260	chr20:52647830-52663783	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
27	nsv586261	chr20:52647830-52664869	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
28	nsv586267	chr20:52648368-52660741	Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
29	nsv586268	chr20:52648368-52663409	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
30	nsv1066172	chr20:52651154-52662562	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
31	nsv1055306	chr20:52651154-52666885	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
32	nsv1063512	chr20:52651609-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
33	nsv1067083	chr20:52651609-52665631	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
34	nsv179659	chr20:52651946-52661376	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
35	nsv1065957	chr20:52651963-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
36	nsv1060202	chr20:52652050-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
37	nsv1061631	chr20:52652346-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
38	nsv1062635	chr20:52652471-52662562	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
39	nsv586272	chr20:52652855-52660741	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
40	nsv586277	chr20:52654219-52660741	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 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	chr20:52657800-52659600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:52657800-52664800	Weak transcription	HSMMtube	muscle
7	chr20:52658600-52660000	Enhancers	K562	blood
8	chr20:52659400-52660400	Enhancers	Fetal Stomach	stomach
9	chr20:52659400-52661000	Enhancers	NHDF-Ad	bronchial

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