Variant report

Variant	rs709045
Chromosome Location	chr20:29965014-29965015
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:29960399..29962900-chr20:29964371..29965877,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DEFB119-1	chr20:29964966-29965242	NONHSAT079289
2	lnc-DEFB119-1	chr20:29964966-29965242	NR_073153
3	lnc-DEFB119-1	chr20:29964966-29965165	NONHSAT079290

Extended variants
information (count: 128 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1075852	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1080568	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1474945	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1884743	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1980582	0.80[ASN][1000 genomes]
rs2076373	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2076374	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap]
rs2076375	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2143191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2145077	0.90[ASN][1000 genomes]
rs2145078	0.85[JPT][hapmap]
rs2180566	0.89[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs2206381	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2206382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2206383	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2223527	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2273468	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2281554	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs2295500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2376538	0.83[EUR][1000 genomes]
rs2376858	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs35293804	0.81[EUR][1000 genomes]
rs3761199	0.82[YRI][hapmap]
rs4243975	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4300919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4333000	0.80[ASN][1000 genomes]
rs4525766	0.89[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4911191	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4911211	0.81[EUR][1000 genomes]
rs4911274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4911306	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs4911328	1.00[YRI][hapmap]
rs4911329	0.89[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs4911337	0.90[ASN][1000 genomes]
rs4911432	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4911529	0.80[ASN][1000 genomes]
rs4911531	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4911555	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4911557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5001275	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs56391357	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6057649	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6057704	0.99[ASN][1000 genomes]
rs6057860	0.81[EUR][1000 genomes]
rs6058531	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6058918	0.84[JPT][hapmap]
rs6059128	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs6059238	0.81[EUR][1000 genomes]
rs6059263	0.93[ASN][1000 genomes]
rs6059335	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6059379	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs6059955	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6061178	0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs6061207	0.82[ASN][1000 genomes]
rs6061213	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs6087445	0.89[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs6087464	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap]
rs6087468	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6087493	0.87[ASN][1000 genomes]
rs6087777	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6087831	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6087854	0.81[EUR][1000 genomes]
rs6087927	0.87[ASN][1000 genomes]
rs6088036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6088076	0.99[ASN][1000 genomes]
rs6088077	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6088109	0.89[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs6088112	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6088144	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6088146	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6088147	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6088148	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6088167	0.80[EUR][1000 genomes]
rs6088215	0.89[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs6088227	0.87[ASN][1000 genomes]
rs6088264	0.81[EUR][1000 genomes]
rs6088748	0.84[EUR][1000 genomes]
rs6089126	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs6141536	0.82[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs6141934	0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6141980	0.88[EUR][1000 genomes]
rs6142150	0.82[EUR][1000 genomes]
rs6142220	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6142241	0.83[EUR][1000 genomes]
rs721220	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs721221	0.93[ASN][1000 genomes]
rs734418	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs760996	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs975075	0.94[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869384	chr20:29833386-30605088	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
2	nsv470546	chr20:29833609-30235302	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
3	nsv1066779	chr20:29833958-29981427	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv544229	chr20:29833958-29981427	Weak transcription ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1060567	chr20:29833958-29992219	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv544230	chr20:29833958-29992219	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1059642	chr20:29833958-30024839	Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544231	chr20:29833958-30024839	Active TSS Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1055527	chr20:29833958-30078925	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1062069	chr20:29833958-30153486	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv1062612	chr20:29833958-30219337	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
12	nsv1061673	chr20:29833958-30649496	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
13	nsv544232	chr20:29833958-30649496	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
14	nsv1063413	chr20:29835037-29969913	ZNF genes & repeats Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1065102	chr20:29835037-30011213	ZNF genes & repeats Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1058516	chr20:29835037-30024168	ZNF genes & repeats Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1058344	chr20:29835037-30386611	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	402 gene(s)	inside rSNPs	diseases
18	nsv1059672	chr20:29835037-30621271	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
19	esv2763228	chr20:29835049-30239522	Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
20	nsv949085	chr20:29846303-30473188	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	414 gene(s)	inside rSNPs	diseases
21	nsv1060247	chr20:29860167-29969913	ZNF genes & repeats Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv1065659	chr20:29877877-30020310	ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv544234	chr20:29877877-30020310	Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv1058639	chr20:29877877-30101083	Weak transcription Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
25	nsv544235	chr20:29877877-30101083	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
26	nsv1058020	chr20:29877877-30197681	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
27	nsv544236	chr20:29877877-30197681	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
28	nsv1063560	chr20:29877877-30435888	Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
29	nsv544237	chr20:29877877-30435888	Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
30	nsv1066621	chr20:29877992-30052439	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
31	nsv482272	chr20:29884928-30043331	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
32	nsv585910	chr20:29893501-30045393	Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
33	nsv458961	chr20:29893501-30275906	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
34	nsv585911	chr20:29893501-30275906	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
35	nsv1067177	chr20:29900572-30299363	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
36	nsv912835	chr20:29912852-30053255	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
37	nsv1060041	chr20:29926828-30016443	Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
38	nsv979426	chr20:29964176-29965111	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs709045	FRG1B	cis	parietal	SCAN
rs709045	MAP1LC3A	cis	parietal	SCAN
rs709045	FRG1B	cis	cerebellum	SCAN
rs709045	DNMT3B	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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