Variant report

Variant	rs6079537
Chromosome Location	chr20:14697386-14697387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10446030	0.87[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13044671	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2180476	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2224274	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4278992	0.87[AMR][1000 genomes]
rs4814319	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4814324	0.96[CEU][hapmap];0.86[GIH][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6074776	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6074777	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6074778	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6074779	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6074784	0.96[CEU][hapmap]
rs6074786	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6074787	0.96[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6074788	0.96[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6074789	0.96[CEU][hapmap]
rs6074798	0.87[ASW][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6079536	0.81[EUR][1000 genomes]
rs6079540	0.96[CEU][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079543	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6079544	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079545	0.96[CEU][hapmap]
rs6079547	0.96[CEU][hapmap]
rs6079549	0.96[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079551	0.96[CEU][hapmap]
rs6079553	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs6110421	0.96[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs980319	1.00[ASW][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:70 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv529577	chr20:14434373-14799157	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1060985	chr20:14488785-14759939	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1059579	chr20:14518849-14941319	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1065590	chr20:14549721-14848061	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3512353	chr20:14560028-15087709	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3512354	chr20:14560087-15087661	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1055559	chr20:14560892-14748546	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv534569	chr20:14567155-14700099	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv993469	chr20:14567155-14799157	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv585452	chr20:14569942-14986602	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv912695	chr20:14579703-14992542	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1063430	chr20:14593867-14698300	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv585453	chr20:14609957-14936935	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv585454	chr20:14609957-14967506	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv912696	chr20:14626845-14723009	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1055668	chr20:14627662-14698300	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1066070	chr20:14627662-15180181	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv1056497	chr20:14628216-14910061	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1060876	chr20:14629122-14875771	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv544189	chr20:14629122-14875771	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv932622	chr20:14629123-14776939	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv533082	chr20:14629123-14799157	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv869474	chr20:14629123-14838276	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv868932	chr20:14629123-14928627	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv1062048	chr20:14633652-14887370	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv912697	chr20:14637084-14731595	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	esv2751906	chr20:14658364-15026100	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
29	nsv458877	chr20:14658870-14781684	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
30	nsv585455	chr20:14658870-14781684	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
31	nsv1055506	chr20:14667415-14748546	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
32	nsv949548	chr20:14667415-15125972	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
33	nsv948395	chr20:14667415-15161670	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
34	nsv869659	chr20:14668182-14726777	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
35	nsv517126	chr20:14668243-14714457	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
36	nsv585456	chr20:14668243-14954943	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
37	nsv585457	chr20:14672177-14758111	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
38	nsv912698	chr20:14672177-14890211	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
39	nsv912699	chr20:14672177-14901776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
40	nsv1055619	chr20:14675588-14721127	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
41	nsv1059534	chr20:14677058-14848061	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
42	nsv544190	chr20:14677058-14848061	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
43	nsv1058831	chr20:14677058-14941319	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
44	nsv544191	chr20:14677058-14941319	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
45	nsv912700	chr20:14678135-14739839	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
46	nsv1057588	chr20:14681510-14721127	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
47	nsv1067276	chr20:14681510-14732301	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
48	nsv1063055	chr20:14681510-14739573	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
49	nsv1058942	chr20:14681510-14762971	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
50	esv2755548	chr20:14681863-14760044	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6079537	SNRPB2	cis	parietal	SCAN
rs6079537	C20orf71	trans	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14681600-14698200	Weak transcription	Fetal Kidney	kidney
2	chr20:14693200-14698400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:14693400-14698200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr20:14693600-14697800	Weak transcription	Fetal Intestine Large	intestine
5	chr20:14693800-14698200	Weak transcription	Fetal Lung	lung
6	chr20:14694200-14697600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:14694200-14697600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr20:14694200-14698600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:14694400-14698400	Weak transcription	Stomach Mucosa	stomach
10	chr20:14694400-14700400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:14695400-14698400	Weak transcription	Pancreas	Pancrea
12	chr20:14696000-14697600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:14696200-14697400	Enhancers	Fetal Brain Male	brain
14	chr20:14696200-14698600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr20:14696400-14697400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr20:14696400-14697400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr20:14696400-14697600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr20:14696400-14697600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr20:14696800-14697400	Enhancers	Brain Germinal Matrix	brain
20	chr20:14696800-14697600	Enhancers	H9 Cell Line	embryonic stem cell
21	chr20:14696800-14697600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr20:14697000-14697400	Flanking Active TSS	Fetal Brain Female	brain
23	chr20:14697000-14699200	Enhancers	Fetal Intestine Small	intestine
24	chr20:14697200-14697400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr20:14697200-14697400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr20:14697200-14697400	Enhancers	Brain Anterior Caudate	brain
27	chr20:14697200-14697600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr20:14697200-14697600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr20:14697200-14697600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr20:14697200-14697600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr20:14697200-14697600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr20:14697200-14698000	Enhancers	A549	lung
33	chr20:14697200-14698800	Enhancers	Liver	Liver

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