Variant report

Variant	rs4246160
Chromosome Location	chr9:43396938-43396939
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10796613	0.83[AMR][1000 genomes]
rs2928515	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4246161	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4246162	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4427280	0.83[AMR][1000 genomes]
rs4961792	0.87[AMR][1000 genomes]
rs4961873	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:80 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893173	chr9:43034822-43998470	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv1829975	chr9:43045290-43831337	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1032639	chr9:43064834-43701826	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1025182	chr9:43064834-43705240	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1027611	chr9:43064834-43747241	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1027107	chr9:43064834-43776906	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1034498	chr9:43064834-43780897	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1019827	chr9:43064834-43790334	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1030625	chr9:43064834-43800174	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1033674	chr9:43127213-43776906	Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1016572	chr9:43127213-43800174	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv436621	chr9:43145796-44122367	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1015998	chr9:43166976-43734207	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1020636	chr9:43166976-43795563	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1020348	chr9:43166976-43800174	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv893174	chr9:43180204-43619959	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
17	esv1834582	chr9:43181037-43468853	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region lncRNA	6 gene(s)	inside rSNPs	diseases
18	esv3521726	chr9:43313699-43471054	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region lncRNA	5 gene(s)	inside rSNPs	diseases
19	esv3521727	chr9:43313699-43471054	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS	TF binding region lncRNA	5 gene(s)	inside rSNPs	diseases
20	esv18167	chr9:43313859-43400911	Enhancers Weak transcription	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
21	esv1835465	chr9:43314125-43400052	Enhancers Weak transcription	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv614339	chr9:43314352-43468853	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv614340	chr9:43314352-43469466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv893175	chr9:43314875-43614545	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv893176	chr9:43314875-43668780	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
26	esv3346110	chr9:43315506-43469404	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv515142	chr9:43315660-43785116	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
28	esv3584910	chr9:43315670-43795575	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
29	nsv442543	chr9:43315670-43795575	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
30	nsv1022920	chr9:43315962-43772038	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
31	nsv1025263	chr9:43315962-43776906	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
32	nsv1022381	chr9:43315962-43780897	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
33	nsv1030430	chr9:43315962-43790334	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
34	nsv1020786	chr9:43315962-43795563	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
35	nsv1031843	chr9:43315962-43800174	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
36	nsv1030874	chr9:43315962-44114860	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island lncRNA	16 gene(s)	inside rSNPs	diseases
37	nsv1021270	chr9:43315962-44145340	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island lncRNA	19 gene(s)	inside rSNPs	diseases
38	nsv1024462	chr9:43315962-44205637	Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island lncRNA	20 gene(s)	inside rSNPs	diseases
39	esv1840571	chr9:43321166-43400052	Enhancers Weak transcription	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
40	nsv614345	chr9:43321166-43469801	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
41	nsv614346	chr9:43321166-43470341	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
42	nsv893177	chr9:43321166-43619959	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
43	nsv893178	chr9:43321166-43737633	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
44	nsv893179	chr9:43321166-43998470	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island lncRNA	11 gene(s)	inside rSNPs	diseases
45	esv1836150	chr9:43353062-43400819	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
46	esv1839730	chr9:43353062-43400819	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
47	esv1840127	chr9:43353062-43400819	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
48	esv1841118	chr9:43353062-43400819	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
49	esv1841551	chr9:43353062-43400819	Enhancers Weak transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
50	nsv614349	chr9:43353062-43444135	Enhancers Weak transcription Bivalent Enhancer	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4246160	CNTNAP3B	cis	Nerve Tibial	GTEx
rs4246160	ANKRD20A7P	cis	Artery Tibial	GTEx
rs4246160	CR848007.2	cis	Adipose Subcutaneous	GTEx
rs4246160	ANKRD20A7P	cis	Thyroid	GTEx
rs4246160	ANKRD20A7P	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:43396400-43399000	Enhancers	Primary B cells from peripheral blood	blood

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