Variant report

Variant	rs3757859
Chromosome Location	chr7:100241163-100241164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:100240778-100241434	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr7:100241154-100241201	HepG2	liver:	n/a	n/a
3	RAD21	chr7:100241154-100241462	HepG2	liver:	n/a	chr7:100241304-100241313
4	RAD21	chr7:100241124-100241499	MCF-7	breast:	n/a	chr7:100241304-100241313

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:100238260..100241603-chr7:100301224..100306213,4	K562	blood:
2	chr7:100235870..100241765-chr7:100269603..100274523,10	K562	blood:
3	chr7:100240447..100242997-chr7:100251202..100253123,2	K562	blood:
4	chr7:100207856..100215304-chr7:100235701..100242038,10	K562	blood:
5	chr7:100182236..100184425-chr7:100238898..100241261,2	MCF-7	breast:
6	chr7:100223053..100226003-chr7:100238727..100241235,2	MCF-7	breast:
7	chr7:100024854..100029212-chr7:100238393..100241596,5	K562	blood:
8	chr7:100025315..100028678-chr7:100237515..100241293,6	K562	blood:
9	chr7:100228020..100230083-chr7:100240637..100244501,3	K562	blood:
10	chr7:100223071..100228603-chr7:100236890..100242224,6	K562	blood:
11	chr7:100200627..100204986-chr7:100237375..100241909,8	K562	blood:
12	chr7:100238702..100243589-chr7:100269441..100273725,6	MCF-7	breast:
13	chr7:100234354..100241214-chr7:100269812..100274154,10	K562	blood:
14	chr7:100209391..100211157-chr7:100240305..100242617,2	MCF-7	breast:
15	chr7:100238851..100242571-chr7:100242728..100246485,5	K562	blood:
16	chr7:100183091..100184798-chr7:100238306..100241212,2	K562	blood:
17	chr7:100240313..100241919-chr7:100244604..100246512,2	K562	blood:
18	chr7:100183091..100185790-chr7:100237185..100241212,3	K562	blood:
19	chr7:100200263..100204018-chr7:100237004..100241425,9	K562	blood:

No data

Variant related genes	Relation type
TFR2	TF binding region
ENSG00000172354	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000077080	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000172336	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10247962	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1052897	1.00[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12673102	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1734907	1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs221770	1.00[JPT][hapmap];0.90[LWK][hapmap]
rs221774	1.00[JPT][hapmap]
rs221780	1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs221784	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs221786	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs221789	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs221797	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs221803	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs4727457	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4729598	1.00[ASW][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4729600	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4988606	0.83[AMR][1000 genomes]
rs506597	1.00[JPT][hapmap]
rs564449	1.00[JPT][hapmap]
rs6975957	1.00[JPT][hapmap]
rs7457868	0.93[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[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	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv607934	chr7:100240505-100271521	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3757859	CYP3A43	cis	parietal	SCAN
rs3757859	ZNF3	cis	parietal	SCAN
rs3757859	BUD31	cis	cerebellum	SCAN
rs3757859	TFR2	cis	lymphoblastoid	seeQTL
rs3757859	MOGAT3	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100231400-100242400	Weak transcription	Right Atrium	heart
2	chr7:100231400-100247200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:100237600-100241200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:100238000-100241400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr7:100238400-100252600	Weak transcription	Gastric	stomach
6	chr7:100238600-100244600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:100239400-100241400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:100240200-100241400	Enhancers	Esophagus	oesophagus
9	chr7:100240400-100245800	Weak transcription	Brain Anterior Caudate	brain
10	chr7:100240600-100241400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:100240600-100241400	Enhancers	K562	blood
12	chr7:100240600-100248200	Strong transcription	Fetal Brain Female	brain
13	chr7:100240800-100241200	Enhancers	HepG2	liver
14	chr7:100240800-100241400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr7:100240800-100247800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:100241000-100247800	Weak transcription	Pancreas	Pancrea
17	chr7:100241000-100253200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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