Variant report

Variant	rs764444
Chromosome Location	chr20:41210746-41210747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:41210269..41211939-chr20:41214857..41217644,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17747544	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4810361	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6016833	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6030340	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6065515	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6102913	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs6130172	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:45 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1059852	chr20:41087948-41217672	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv544276	chr20:41087948-41217672	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1055546	chr20:41102999-41260749	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1064253	chr20:41120425-41379706	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1061449	chr20:41126720-41212178	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv586006	chr20:41157707-41290936	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1065892	chr20:41168686-41230732	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1063513	chr20:41171076-41303205	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1056430	chr20:41171814-41243487	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv586009	chr20:41174105-41254693	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv870259	chr20:41174537-41251308	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv458978	chr20:41174693-41230763	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv586010	chr20:41174693-41230763	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv586011	chr20:41174693-41243236	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv912875	chr20:41174693-41254183	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv519654	chr20:41174693-41254693	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv912876	chr20:41174693-41296994	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv432118	chr20:41175615-41243286	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv586012	chr20:41176364-41243236	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv1061179	chr20:41178700-41243024	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1057508	chr20:41178700-41243487	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv586013	chr20:41178858-41243236	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv586014	chr20:41178858-41252905	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv432119	chr20:41178886-41243286	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
27	nsv1065411	chr20:41181079-41234914	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv432120	chr20:41181486-41243186	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
29	nsv912877	chr20:41182311-41210746	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv586015	chr20:41182311-41240700	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
31	nsv586016	chr20:41182311-41243236	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
32	nsv586017	chr20:41182311-41261444	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
33	nsv526415	chr20:41184009-41290936	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
34	nsv1063974	chr20:41185138-41292788	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
35	nsv586018	chr20:41188318-41297693	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
36	nsv532517	chr20:41188651-41342196	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
37	nsv1062850	chr20:41202830-41239845	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
38	nsv528161	chr20:41202935-41297693	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
39	nsv1055754	chr20:41205911-41243487	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
40	nsv1057302	chr20:41206845-41243487	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
41	nsv586019	chr20:41207365-41241888	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
42	nsv586020	chr20:41207365-41243236	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
43	nsv949644	chr20:41207365-41333541	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
44	nsv458979	chr20:41210746-41243236	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
45	nsv586021	chr20:41210746-41243236	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs764444	SPINT3	cis	cerebellum	SCAN
rs764444	C20orf165	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41206800-41216200	Weak transcription	Gastric	stomach
2	chr20:41207400-41215400	Weak transcription	Pancreas	Pancrea
3	chr20:41207400-41218600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr20:41209800-41210800	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr20:41210000-41210800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr20:41210400-41210800	Enhancers	H1 Cell Line	embryonic stem cell

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