Variant report

Variant	rs979348
Chromosome Location	chr5:97074135-97074136
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2215E18.1.1-6	chr5:97073598-97074617	NONHSAT102935

Extended variants
information (count: 265 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11135526	0.88[ASN][1000 genomes]
rs12651959	0.88[ASN][1000 genomes]
rs12658392	0.88[ASN][1000 genomes]
rs12658613	0.88[ASN][1000 genomes]
rs1304337	0.87[ASN][1000 genomes]
rs1429862	0.85[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.88[ASN][1000 genomes]
rs1429863	0.80[CHD][hapmap];0.87[ASN][1000 genomes]
rs17087767	0.87[ASN][1000 genomes]
rs17087793	0.87[ASN][1000 genomes]
rs35004760	0.93[ASN][1000 genomes]
rs3888857	0.91[ASN][1000 genomes]
rs4549551	0.93[ASN][1000 genomes]
rs4573015	0.90[ASN][1000 genomes]
rs4594877	0.93[ASN][1000 genomes]
rs55957494	0.88[ASN][1000 genomes]
rs56201228	0.90[ASN][1000 genomes]
rs6557001	0.87[ASN][1000 genomes]
rs66658311	0.91[ASN][1000 genomes]
rs67143861	0.91[ASN][1000 genomes]
rs67317808	0.91[ASN][1000 genomes]
rs67323908	0.91[ASN][1000 genomes]
rs68075227	0.94[ASN][1000 genomes]
rs6883166	0.88[ASN][1000 genomes]
rs72777739	0.87[ASN][1000 genomes]
rs72777740	0.88[ASN][1000 genomes]
rs72777747	0.94[ASN][1000 genomes]
rs72777759	0.91[ASN][1000 genomes]
rs72777789	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72777791	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72777792	0.90[ASN][1000 genomes]
rs72777793	0.90[ASN][1000 genomes]
rs7718732	0.87[ASN][1000 genomes]
rs7721157	0.87[ASN][1000 genomes]
rs7723898	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:231 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534326	chr5:96531217-97283481	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv882394	chr5:96538585-97108559	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1031429	chr5:96777286-97269498	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv527650	chr5:96783726-97260358	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1028224	chr5:96791214-97258383	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv537814	chr5:96791214-97258383	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv882396	chr5:96849023-97126520	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv830417	chr5:96915211-97129196	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv598965	chr5:96934739-97101816	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1020125	chr5:96937248-97350644	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv462256	chr5:96940843-97096042	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv598966	chr5:96940843-97096042	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv2755089	chr5:96992975-97099320	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv598968	chr5:97005141-97096042	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv462257	chr5:97005141-97108559	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv598969	chr5:97005141-97108559	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv432757	chr5:97006304-97213768	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv432758	chr5:97013452-97099320	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv2754965	chr5:97013452-97296147	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv598971	chr5:97027486-97096042	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv462258	chr5:97027486-97108626	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv598972	chr5:97027486-97108626	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv517188	chr5:97027486-97137056	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	esv2752865	chr5:97028084-97099320	Active TSS Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	esv2753403	chr5:97028084-97099320	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	esv2754896	chr5:97028084-97099320	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	esv2755514	chr5:97028084-97099320	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
28	esv2755643	chr5:97028084-97099320	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
29	esv2755759	chr5:97028084-97099320	Enhancers ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
30	esv2752084	chr5:97028429-97099320	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
31	esv2752638	chr5:97028429-97099320	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
32	esv2754348	chr5:97028429-97099320	Weak transcription ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
33	esv2756134	chr5:97028429-97099320	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
34	nsv432759	chr5:97028429-97099320	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
35	esv2757122	chr5:97028429-97138147	Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
36	esv2759356	chr5:97028429-97138147	Active TSS Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
37	esv2752992	chr5:97030575-97099320	Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
38	esv2753970	chr5:97030575-97099320	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
39	nsv432760	chr5:97030575-97099320	Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
40	esv2752085	chr5:97030575-97099344	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
41	nsv882399	chr5:97030575-97101816	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
42	nsv882400	chr5:97030575-97108559	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
43	nsv432767	chr5:97030575-97125963	Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
44	nsv432770	chr5:97030575-97138147	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
45	nsv432761	chr5:97030575-97165254	Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
46	nsv1027714	chr5:97034552-97211333	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
47	nsv598976	chr5:97035541-97082417	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
48	nsv598977	chr5:97035541-97096042	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
49	nsv1031159	chr5:97041187-97099320	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
50	nsv1034500	chr5:97041187-97099672	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs979348	ESPNL	trans	brain	seeQTL
rs979348	PCP2	trans	brain	seeQTL
rs979348	ZFPM2	trans	brain	seeQTL
rs979348	IL16	trans	brain	seeQTL
rs979348	CRTAM	trans	brain	seeQTL
rs979348	AMICA1	trans	brain	seeQTL
rs979348	BARHL1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:97069000-97075000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:97072600-97075200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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