Variant report

Variant	rs6665129
Chromosome Location	chr1:228140460-228140461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228139817-228142070	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:228139397-228141971	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:
2	chr1:228135018..228137488-chr1:228138283..228141260,2	K562	blood:
3	chr1:228055780..228058656-chr1:228138484..228140779,2	MCF-7	breast:
4	chr1:228139640..228141496-chr1:228143791..228146125,2	MCF-7	breast:
5	chr1:227946584..227948146-chr1:228139573..228141721,2	MCF-7	breast:

No data

Variant related genes	Relation type
WNT9A	TF binding region
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1034792	0.83[CEU][hapmap]
rs11579417	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs11580665	0.90[CEU][hapmap]
rs11589040	0.91[CEU][hapmap];0.88[TSI][hapmap]
rs11589467	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs11589513	0.83[CEU][hapmap]
rs11590118	0.90[CEU][hapmap]
rs13374948	0.90[CEU][hapmap]
rs2107906	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3949294	0.91[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4399155	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4653533	0.81[CEU][hapmap]
rs4653894	1.00[CEU][hapmap]
rs57824519	0.87[EUR][1000 genomes]
rs6426487	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6672422	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs6672559	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs74140812	0.87[EUR][1000 genomes]
rs74140813	0.89[EUR][1000 genomes]
rs74140814	0.89[EUR][1000 genomes]
rs74143604	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7539664	0.83[CEU][hapmap]
rs8192629	0.87[EUR][1000 genomes]
rs9287010	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
9	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv947387	chr1:228140028-228206630	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6665129	ACBD3	cis	cerebellum	SCAN
rs6665129	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228136800-228141000	Weak transcription	Ovary	ovary
2	chr1:228136800-228141000	Weak transcription	NHDF-Ad	bronchial
3	chr1:228137000-228141000	Weak transcription	HSMMtube	muscle
4	chr1:228137200-228140600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:228137200-228141000	Weak transcription	HSMM	muscle
6	chr1:228138000-228141000	Weak transcription	Fetal Lung	lung
7	chr1:228139400-228142000	Bivalent Enhancer	Fetal Stomach	stomach
8	chr1:228139600-228142200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:228139800-228142000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:228140000-228140800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:228140200-228141200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:228140200-228141800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr1:228140200-228142000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:228140200-228142000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr1:228140400-228141600	Weak transcription	Esophagus	oesophagus
16	chr1:228140400-228142000	Bivalent Enhancer	Fetal Muscle Leg	muscle

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