Variant report

Variant	rs687949
Chromosome Location	chr15:41183145-41183146
allele	C/T
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	MEF2A	chr15:41182937-41183255	GM12878	blood:	n/a	chr15:41182991-41183005
2	POU2F2	chr15:41182749-41183182	GM12878	blood:	n/a	chr15:41182954-41182962 chr15:41182951-41182965 chr15:41182949-41182967 chr15:41182953-41182963 chr15:41182951-41182963 chr15:41182952-41182962 chr15:41182954-41182961 chr15:41182953-41182962 chr15:41182951-41182964 chr15:41182953-41182964 chr15:41182952-41182962 chr15:41182950-41182965
3	EBF1	chr15:41182874-41183577	GM12878	blood:	n/a	n/a
4	ZNF143	chr15:41183008-41183149	GM12878	blood:	n/a	n/a
5	MXI1	chr15:41182906-41183167	GM12878	blood:	n/a	n/a
6	POU2F2	chr15:41182962-41183292	GM12891	blood:	n/a	n/a
7	TBP	chr15:41182960-41183250	GM12878	blood:	n/a	n/a
8	CHD2	chr15:41183017-41183184	GM12878	blood:	n/a	n/a
9	RUNX3	chr15:41182972-41183303	GM12878	blood:	n/a	n/a
10	STAT1	chr15:41183071-41183436	GM12878	blood:	n/a	n/a
11	EBF1	chr15:41182976-41183226	GM12878	blood:	n/a	n/a
12	SIN3A	chr15:41183094-41183277	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41136414..41139864-chr15:41181356..41186359,5	MCF-7	breast:
2	chr15:41151290..41151919-chr15:41182973..41183489,2	MCF-7	breast:
3	chr15:41164990..41168154-chr15:41182067..41186138,6	MCF-7	breast:
4	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS18-2	chr15:41182850-41183627	NONHSAT041893

Variant related genes	Relation type
VPS18	TF binding region
ENSG00000104140	Chromatin interaction
ENSG00000264256	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000261183	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11635602	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971177	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16971186	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16971188	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2445489	0.82[ASN][1000 genomes]
rs2445490	0.94[ASN][1000 genomes]
rs2934172	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3100810	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743036	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4552004	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs595559	1.00[EUR][1000 genomes]
rs601436	0.86[ASN][1000 genomes]
rs601696	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615987	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616606	0.86[ASN][1000 genomes]
rs618892	0.86[ASN][1000 genomes]
rs618916	0.86[ASN][1000 genomes]
rs677273	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694213	1.00[EUR][1000 genomes]
rs7172280	0.88[ASN][1000 genomes]
rs8024861	0.86[ASN][1000 genomes]
rs8024961	0.86[ASN][1000 genomes]
rs8025867	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41172000-41184000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr15:41177200-41184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:41177400-41186000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:41182200-41183800	Weak transcription	Placenta	Placenta
5	chr15:41182800-41183400	Flanking Active TSS	GM12878-XiMat	blood
6	chr15:41183000-41183200	Enhancers	Esophagus	oesophagus
7	chr15:41183000-41185800	Enhancers	Hela-S3	cervix

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