Variant report

Variant	rs56778757
Chromosome Location	chr4:122290719-122290720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNIP3-2	chr4:122290588-122291500	NONHSAT098140

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10030200	0.98[ASN][1000 genomes]
rs12642412	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12651280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56733280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59502268	1.00[AFR][1000 genomes]
rs62320777	0.92[ASN][1000 genomes]
rs62320783	0.92[ASN][1000 genomes]
rs692249	0.98[ASN][1000 genomes]
rs692496	0.98[ASN][1000 genomes]
rs72668982	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1003747	chr4:122273631-122291131	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases
7	nsv1014710	chr4:122273631-122292143	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv437422	chr4:122276876-122291522	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv508308	chr4:122278897-122312719	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv10559	chr4:122281398-122292297	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv3511588	chr4:122281552-122290950	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	diseases
12	esv2539204	chr4:122281761-122290800	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	diseases
13	nsv1003477	chr4:122281973-122297539	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1001654	chr4:122282456-122297539	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1012376	chr4:122282456-122299460	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	esv3467684	chr4:122284902-122291400	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases
17	esv3467685	chr4:122284902-122291400	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases
18	nsv528104	chr4:122285263-122291522	Enhancers Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv595343	chr4:122285263-122291522	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv966316	chr4:122289350-122291731	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122282200-122294000	Weak transcription	HMEC	breast
2	chr4:122282200-122295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:122290600-122290800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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