Variant report

Variant	rs56910871
Chromosome Location	chr1:153698703-153698704
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr1:153698468-153698764	ECC-1	luminal epithelium:	n/a	n/a
2	FOXA1	chr1:153698458-153698894	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:153698391-153698717	A549	lung:	n/a	n/a
4	NR3C1	chr1:153698442-153698807	ECC-1	luminal epithelium:	n/a	n/a
5	FOXA1	chr1:153698354-153698713	A549	lung:	n/a	n/a
6	NR3C1	chr1:153698411-153698814	A549	lung:	n/a	n/a
7	NR3C1	chr1:153698542-153698870	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153641515..153644992-chr1:153698475..153702164,4	MCF-7	breast:
2	chr1:153697814..153700454-chr1:153732023..153734328,2	K562	blood:
3	chr1:153651109..153660855-chr1:153698392..153702896,14	MCF-7	breast:
4	chr1:153698690..153700726-chr1:153934650..153936976,2	MCF-7	breast:
5	chr1:153641911..153645780-chr1:153697153..153701509,4	MCF-7	breast:
6	chr1:153536608..153541746-chr1:153698648..153702694,5	MCF-7	breast:

No data

Variant related genes	Relation type
INTS3	TF binding region
ENSG00000143570	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000169418	Chromatin interaction
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11264299	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264336	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132619	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12062022	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12068901	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12070179	0.94[EUR][1000 genomes]
rs12070559	0.89[EUR][1000 genomes]
rs12071801	0.89[EUR][1000 genomes]
rs12076697	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097043	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12097583	0.94[EUR][1000 genomes]
rs28730729	1.00[ASN][1000 genomes]
rs28730731	1.00[ASN][1000 genomes]
rs35240348	1.00[ASN][1000 genomes]
rs36064263	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3891075	1.00[ASN][1000 genomes]
rs4073768	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41265168	1.00[ASN][1000 genomes]
rs41265191	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845359	1.00[ASN][1000 genomes]
rs55658698	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55778008	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56167936	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57314764	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57482283	1.00[ASN][1000 genomes]
rs60100741	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60316596	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60827720	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61803563	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803565	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803566	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803567	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803571	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803573	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61805738	1.00[ASN][1000 genomes]
rs61806710	1.00[ASN][1000 genomes]
rs61806714	1.00[ASN][1000 genomes]
rs61806719	1.00[ASN][1000 genomes]
rs6427085	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660232	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663011	0.89[EUR][1000 genomes]
rs6663988	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668229	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672371	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682411	0.90[EUR][1000 genomes]
rs6687602	0.94[EUR][1000 genomes]
rs6689176	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115713	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7512561	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515716	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520045	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520235	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533987	1.00[ASN][1000 genomes]
rs7556155	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556379	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556575	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8532	1.00[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	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription 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
3	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers 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 miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer 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	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
10	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
13	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
14	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
17	nsv1002328	chr1:153672031-153718746	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56910871	SLC27A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153687400-153699800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:153690400-153699000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:153697800-153699800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:153697800-153699800	Enhancers	Fetal Kidney	kidney
5	chr1:153697800-153700000	Weak transcription	Right Atrium	heart
6	chr1:153698000-153699800	Enhancers	HepG2	liver
7	chr1:153698200-153698800	Enhancers	Adipose Nuclei	Adipose
8	chr1:153698200-153699400	Weak transcription	Pancreas	Pancrea
9	chr1:153698600-153698800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:153698600-153699800	Enhancers	A549	lung
11	chr1:153698600-153699800	Enhancers	Hela-S3	cervix

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