Variant report

Variant	rs3803312
Chromosome Location	chr14:105071815-105071816
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr14:105071036-105071864	PANC-1	pancreas:	n/a	chr14:105071234-105071247 chr14:105071237-105071250 chr14:105071230-105071250 chr14:105071744-105071754 chr14:105071231-105071249 chr14:105071232-105071242 chr14:105071230-105071244 chr14:105071486-105071494 chr14:105071230-105071250 chr14:105071230-105071250 chr14:105071236-105071245 chr14:105071234-105071247 chr14:105071241-105071250 chr14:105071737-105071751
2	REST	chr14:105070748-105071929	MCF-7	breast:	n/a	chr14:105071234-105071247 chr14:105070752-105070762 chr14:105071237-105071250 chr14:105071230-105071250 chr14:105071744-105071754 chr14:105071231-105071249 chr14:105071232-105071242 chr14:105071230-105071244 chr14:105071486-105071494 chr14:105071230-105071250 chr14:105071230-105071250 chr14:105071236-105071245 chr14:105071234-105071247 chr14:105071241-105071250 chr14:105071737-105071751
3	REST	chr14:105070734-105071824	ECC-1	luminal epithelium:	n/a	chr14:105071234-105071247 chr14:105070752-105070762 chr14:105071237-105071250 chr14:105071230-105071250 chr14:105071744-105071754 chr14:105071231-105071249 chr14:105071232-105071242 chr14:105071230-105071244 chr14:105071486-105071494 chr14:105071230-105071250 chr14:105071230-105071250 chr14:105071236-105071245 chr14:105071234-105071247 chr14:105071241-105071250 chr14:105071737-105071751
4	REST	chr14:105070781-105071845	HL-60	blood:	n/a	chr14:105071234-105071247 chr14:105071237-105071250 chr14:105071230-105071250 chr14:105071744-105071754 chr14:105071231-105071249 chr14:105071232-105071242 chr14:105071230-105071244 chr14:105071486-105071494 chr14:105071230-105071250 chr14:105071230-105071250 chr14:105071236-105071245 chr14:105071234-105071247 chr14:105071241-105071250 chr14:105071737-105071751

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C14orf180-2	chr14:105071099-105072888	NONHSAT040264

Variant related genes	Relation type
TMEM179	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10129754	0.98[ASN][1000 genomes]
rs10135130	0.98[ASN][1000 genomes]
rs10136937	0.98[ASN][1000 genomes]
rs10137691	0.98[ASN][1000 genomes]
rs10138987	0.86[ASN][1000 genomes]
rs10144804	0.99[ASN][1000 genomes]
rs10145420	0.86[ASN][1000 genomes]
rs10151692	0.98[ASN][1000 genomes]
rs10151872	0.98[ASN][1000 genomes]
rs10873548	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11160812	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11625738	0.95[ASN][1000 genomes]
rs11625777	0.86[ASN][1000 genomes]
rs11628111	0.98[ASN][1000 genomes]
rs11628289	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11629201	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12101271	0.82[ASN][1000 genomes]
rs12101275	0.82[ASN][1000 genomes]
rs12101279	0.82[ASN][1000 genomes]
rs12879330	0.82[ASN][1000 genomes]
rs12880146	0.86[ASN][1000 genomes]
rs12880486	0.98[ASN][1000 genomes]
rs12880651	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12892016	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28656783	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34527763	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35960466	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3803313	0.99[ASN][1000 genomes]
rs3803315	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3803316	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803317	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809457	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs3809458	0.82[ASN][1000 genomes]
rs3809459	0.82[ASN][1000 genomes]
rs3809460	0.81[ASN][1000 genomes]
rs3809461	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4340263	0.98[ASN][1000 genomes]
rs4454893	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6576053	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6576054	0.86[ASN][1000 genomes]
rs7142224	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs7145273	0.98[ASN][1000 genomes]
rs7146030	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7147154	0.85[ASN][1000 genomes]
rs7148772	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs7148960	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs7155060	0.81[ASN][1000 genomes]
rs7155652	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs8010873	0.85[ASN][1000 genomes]
rs8014246	0.87[ASN][1000 genomes]
rs8017525	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530812	chr14:104775571-105364883	Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1051647	chr14:104983302-105153720	Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv542223	chr14:104983302-105153720	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
4	esv1816766	chr14:105007585-105126354	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv902372	chr14:105011436-105200377	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv902373	chr14:105012858-105078153	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv470676	chr14:105023512-105100021	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv456445	chr14:105023512-105170003	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
9	nsv566047	chr14:105023512-105170003	Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
10	nsv1053591	chr14:105024558-105475931	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
11	nsv542224	chr14:105024558-105475931	Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
12	nsv1044032	chr14:105036464-105124567	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv902374	chr14:105045524-105119784	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv902375	chr14:105045524-105139894	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv902376	chr14:105066444-105100021	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv902377	chr14:105066885-105119784	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	esv3338807	chr14:105069932-105072480	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105071600-105072200	Bivalent Enhancer	Fetal Brain Male	brain
2	chr14:105071800-105072000	Bivalent Enhancer	Fetal Brain Female	brain
3	chr14:105071800-105072400	Bivalent Enhancer	Brain Germinal Matrix	brain
4	chr14:105071800-105073000	Enhancers	Placenta	Placenta
5	chr14:105071800-105077600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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