Variant report

Variant	rs1153845
Chromosome Location	chr15:45724729-45724730
allele	A/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	SIN3AK20	chr15:45724663-45725109	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45723625..45725327-chr15:45926093..45928681,2	MCF-7	breast:
2	chr15:45707965..45711032-chr15:45722401..45726088,3	MCF-7	breast:

Variant related genes	Relation type
MIR147B	TF binding region
ENSG00000171763	Chromatin interaction
ENSG00000137767	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1049508	0.80[MEX][hapmap]
rs1049518	0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10519018	0.91[MEX][hapmap]
rs1060896	0.91[MEX][hapmap]
rs1145076	0.82[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1145077	0.83[GIH][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1145080	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1145084	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1145086	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1145089	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1145091	0.80[MEX][hapmap]
rs1145093	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1145097	0.83[AMR][1000 genomes]
rs1153835	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153855	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1153857	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1153858	0.80[MEX][hapmap]
rs1153860	0.83[AMR][1000 genomes]
rs1153862	0.83[AMR][1000 genomes]
rs11632752	0.91[MEX][hapmap]
rs11632778	0.91[MEX][hapmap]
rs11632920	0.91[MEX][hapmap]
rs11637838	0.91[MEX][hapmap]
rs11637920	0.91[MEX][hapmap]
rs11639420	0.96[MEX][hapmap]
rs12904150	0.91[MEX][hapmap]
rs12908818	0.96[MEX][hapmap]
rs1346267	0.84[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1426932	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1547487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1617634	0.83[AMR][1000 genomes]
rs1617984	0.83[AMR][1000 genomes]
rs1719245	0.83[AMR][1000 genomes]
rs1719246	0.83[AMR][1000 genomes]
rs1719247	0.80[MEX][hapmap]
rs1719250	0.91[MEX][hapmap]
rs2413768	0.96[MEX][hapmap]
rs2413772	0.91[MEX][hapmap]
rs2413774	0.91[MEX][hapmap]
rs2433601	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2433616	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453533	0.83[AMR][1000 genomes]
rs2461700	0.83[AMR][1000 genomes]
rs2461705	0.91[MEX][hapmap]
rs2467853	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2467862	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2467865	0.83[AMR][1000 genomes]
rs2486274	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2486280	0.81[ASN][1000 genomes]
rs2486288	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35861938	0.83[AMR][1000 genomes]
rs6493144	0.95[MEX][hapmap]
rs7167146	0.95[MEX][hapmap]
rs8024620	0.95[MEX][hapmap]
rs8039352	0.87[MEX][hapmap]
rs8039354	0.91[MEX][hapmap]
rs8043258	0.92[CHB][hapmap]
rs872192	0.96[MEX][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1153845	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs1153845	SPATA5L1	cis	multi-tissue	Pritchard
rs1153845	CHST14	cis	parietal	SCAN
rs1153845	GATM	cis	multi-tissue	Pritchard
rs1153845	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs1153845	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs1153845	GATM	cis	cerebellum	SCAN
rs1153845	CTD-2651B20.3	cis	Thyroid	GTEx
rs1153845	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs1153845	BMF	cis	parietal	SCAN
rs1153845	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs1153845	CTD-2651B20.3	cis	Artery Aorta	GTEx
rs1153845	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs1153845	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs1153845	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs1153845	SLC28A2	cis	cerebellum	SCAN
rs1153845	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs1153845	GATM	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45722600-45724800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr15:45722600-45724800	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr15:45722600-45725400	Active TSS	Colonic Mucosa	Colon
4	chr15:45722600-45725400	Active TSS	Rectal Smooth Muscle	rectum
5	chr15:45722600-45727200	Weak transcription	Hela-S3	cervix
6	chr15:45723000-45726000	Weak transcription	Ovary	ovary
7	chr15:45724000-45725600	Weak transcription	Esophagus	oesophagus
8	chr15:45724000-45736800	Weak transcription	Gastric	stomach
9	chr15:45724000-45737200	Weak transcription	Pancreas	Pancrea
10	chr15:45724200-45724800	Enhancers	Fetal Intestine Large	intestine
11	chr15:45724200-45727600	Weak transcription	Stomach Mucosa	stomach
12	chr15:45724400-45725000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:45724400-45725400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
14	chr15:45724400-45727400	Weak transcription	Fetal Intestine Small	intestine
15	chr15:45724600-45725400	Enhancers	Small Intestine	intestine

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