Variant report

Variant	rs3851796
Chromosome Location	chr17:45061175-45061176
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr17:45061154-45061441	GM12878	blood:	n/a	n/a
2	REST	chr17:45061063-45061573	SK-N-SH	brain:	n/a	n/a
3	REST	chr17:45061157-45061456	Hela-S3	cervix:	n/a	n/a
4	REST	chr17:45061105-45061557	HepG2	liver:	n/a	n/a
5	CBX3	chr17:45061150-45061468	K562	blood:	n/a	n/a
6	REST	chr17:45061136-45061608	MCF-7	breast:	n/a	n/a
7	REST	chr17:45061163-45061461	HepG2	liver:	n/a	n/a
8	REST	chr17:45061098-45061569	HL-60	blood:	n/a	n/a
9	REST	chr17:45060942-45061686	HL-60	blood:	n/a	n/a
10	REST	chr17:45061064-45061585	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr17:45061129-45061522	HepG2	liver:	n/a	n/a
12	REST	chr17:45061072-45061599	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr17:45061116-45061508	SK-N-SH	brain:	n/a	n/a
14	TEAD4	chr17:45061122-45061515	A549	lung:	n/a	n/a
15	REST	chr17:45061078-45061520	A549	lung:	n/a	n/a
16	REST	chr17:45061142-45061452	PANC-1	pancreas:	n/a	n/a
17	REST	chr17:45061172-45061448	K562	blood:	n/a	n/a
18	REST	chr17:45061089-45061574	HCT-116	colon:	n/a	n/a
19	REST	chr17:45061104-45061638	PANC-1	pancreas:	n/a	n/a
20	YY1	chr17:45061169-45061546	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F6	chr17:45061143-45061510	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr17:45061146-45061510	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr17:45061044-45061621	PFSK-1	brain:	n/a	n/a
24	REST	chr17:45061013-45061702	ECC-1	luminal epithelium:	n/a	n/a
25	REST	chr17:45061108-45061505	U87	brain:	n/a	n/a
26	REST	chr17:45061155-45061437	HepG2	liver:	n/a	n/a
27	REST	chr17:45061017-45061605	A549	lung:	n/a	n/a
28	REST	chr17:45061123-45061571	MCF-7	breast:	n/a	n/a
29	REST	chr17:45061162-45061509	Hela-S3	cervix:	n/a	n/a
30	REST	chr17:45061170-45061461	PFSK-1	brain:	n/a	n/a
31	REST	chr17:45061004-45061674	ECC-1	luminal epithelium:	n/a	n/a
32	YY1	chr17:45061139-45061498	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr17:45061107-45061562	K562	blood:	n/a	n/a
34	REST	chr17:45061057-45061503	GM12878	blood:	n/a	n/a
35	REST	chr17:45061108-45061507	U87	brain:	n/a	n/a
36	REST	chr17:45061063-45061639	PFSK-1	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:45054920..45059070-chr17:45059993..45065116,7	K562	blood:
2	chr17:45055112..45057937-chr17:45059099..45061766,2	MCF-7	breast:
3	chr17:45055431..45057748-chr17:45059993..45063961,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPRML-3	chr17:45060723-45061435	NONHSAT054237

No data

Variant related genes	Relation type
RPRML	TF binding region
ENSG00000179673	Chromatin interaction
ENSG00000263142	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11079747	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11653589	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653838	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11658863	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12938690	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949446	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952596	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316758	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851792	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851795	1.00[ASN][1000 genomes]
rs3851798	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851799	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4572469	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62073762	0.81[AFR][1000 genomes]
rs7216950	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs8068715	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS 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	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription 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	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3851796	GOSR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45056800-45069000	Weak transcription	Gastric	stomach
2	chr17:45057000-45061200	Weak transcription	Pancreas	Pancrea
3	chr17:45057000-45065600	Weak transcription	Brain Substantia Nigra	brain
4	chr17:45057000-45078400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr17:45057200-45086800	Weak transcription	Right Atrium	heart
6	chr17:45057200-45100000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr17:45057800-45082400	Weak transcription	Brain Angular Gyrus	brain
8	chr17:45058800-45061200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:45059400-45065000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr17:45060200-45078400	Weak transcription	Brain Hippocampus Middle	brain
11	chr17:45060200-45080800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr17:45060400-45061200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:45060400-45061800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr17:45060400-45062800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:45060400-45062800	Enhancers	Fetal Muscle Trunk	muscle
16	chr17:45060400-45063200	Enhancers	HepG2	liver
17	chr17:45061000-45061400	ZNF genes & repeats	Fetal Stomach	stomach
18	chr17:45061000-45062400	Enhancers	Liver	Liver
19	chr17:45061000-45062600	Enhancers	Skeletal Muscle Female	skeletal muscle

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