Variant report

Variant	rs3748556
Chromosome Location	chr1:196926956-196926957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10801575	0.92[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs10801589	0.85[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap]
rs10922163	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1127661	0.80[JPT][hapmap]
rs11589158	0.96[ASN][1000 genomes]
rs1170879	0.85[ASN][1000 genomes]
rs12723250	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734390	0.97[EUR][1000 genomes]
rs12755054	0.85[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs1332667	0.82[ASN][1000 genomes]
rs1412635	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1611982	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1750311	0.85[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1759016	0.89[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2336596	0.82[ASN][1000 genomes]
rs2878749	0.80[JPT][hapmap]
rs34238503	0.87[ASN][1000 genomes]
rs35593284	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748555	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748557	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs3828032	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45489701	0.81[ASN][1000 genomes]
rs55901582	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60002789	0.81[ASN][1000 genomes]
rs6428375	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66511405	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663209	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72468006	0.81[ASN][1000 genomes]
rs7417769	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7522084	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7535993	0.84[ASN][1000 genomes]
rs7541682	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546940	0.84[ASN][1000 genomes]
rs9427652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427664	0.86[ASN][1000 genomes]
rs9427922	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9427934	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727516	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:47 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757766	chr1:196590837-196961802	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv428290	chr1:196590837-196961802	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv1001720	chr1:196658295-196944678	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv535259	chr1:196658295-196944678	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv471614	chr1:196669511-196955230	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	esv1806946	chr1:196673954-196974876	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv1013447	chr1:196697954-196944678	Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
11	nsv535260	chr1:196697954-196944678	Active TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv933234	chr1:196706651-196946907	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	esv2756880	chr1:196709223-197066074	ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
14	nsv8691	chr1:196710764-196927898	Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv872997	chr1:196711067-196933245	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv517662	chr1:196711067-196937536	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	esv1847332	chr1:196723047-196929310	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	esv2764178	chr1:196727850-196939719	Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	esv2750822	chr1:196731148-196993973	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv430124	chr1:196731148-196993973	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	esv34978	chr1:196733133-197011577	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
22	nsv430158	chr1:196733133-197011577	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
23	nsv873019	chr1:196734753-196933245	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv430180	chr1:196739837-197007479	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv873021	chr1:196756300-196933245	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv873024	chr1:196771125-196933245	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	esv3522921	chr1:196779356-196935303	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	esv3522922	chr1:196779356-196935303	Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
29	nsv548826	chr1:196779888-196933245	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
30	nsv873029	chr1:196779888-196933245	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
31	nsv469599	chr1:196796476-196955230	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv482699	chr1:196796476-196955230	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
33	nsv873038	chr1:196799637-196933245	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
34	nsv873049	chr1:196810998-196933245	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
35	nsv1006432	chr1:196816718-196939707	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
36	nsv873055	chr1:196820416-196933245	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
37	nsv467839	chr1:196823030-196933245	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
38	nsv467850	chr1:196823030-196933245	Enhancers Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
39	nsv548851	chr1:196823030-196933245	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
40	nsv548852	chr1:196823030-196937536	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
41	nsv1005113	chr1:196825211-196944678	Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
42	nsv535261	chr1:196825211-196944678	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
43	nsv1003814	chr1:196825211-196982487	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
44	nsv1003573	chr1:196825211-197005106	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
45	nsv873062	chr1:196825863-196933245	Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
46	esv1822192	chr1:196879565-196929552	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
47	esv1792958	chr1:196879565-196940793	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3748556	CFHR3	cis	lung	GTEx
rs3748556	CFHR3	cis	Thyroid	GTEx
rs3748556	CFHR3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196926600-196930200	Strong transcription	Liver	Liver

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