Variant report

Variant	rs4246162
Chromosome Location	chr9:43400929-43400930
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTNAP3B-6	chr9:43399987-43401315	NONHSAT131358

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10796613	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2928515	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246160	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4246161	0.81[ASN][1000 genomes]
rs4427280	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4961792	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4961873	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:62 , 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	nsv614339	chr9:43314352-43468853	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv614340	chr9:43314352-43469466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
22	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
23	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
24	esv3346110	chr9:43315506-43469404	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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
33	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
34	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
35	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
36	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
37	nsv614345	chr9:43321166-43469801	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
38	nsv614346	chr9:43321166-43470341	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
39	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
40	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
41	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
42	nsv614349	chr9:43353062-43444135	Enhancers Weak transcription Bivalent Enhancer	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
43	esv1841350	chr9:43353062-43468579	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
44	esv1838091	chr9:43353062-43468985	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
45	nsv614350	chr9:43353062-43469141	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
46	nsv614365	chr9:43353497-43444135	Bivalent Enhancer Enhancers Weak transcription	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
47	nsv614366	chr9:43353497-43468853	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
48	nsv614367	chr9:43353497-43469141	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
49	nsv614368	chr9:43353497-43469801	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
50	nsv614375	chr9:43353550-43469801	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4246162	ANKRD20A7P	cis	Nerve Tibial	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:43400600-43401000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:43400800-43401000	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links