Variant report

Variant	rs4652492
Chromosome Location	chr1:180218442-180218443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180197450..180200103-chr1:180218151..180221090,2	MCF-7	breast:
2	chr1:180148066..180148643-chr1:180218157..180219119,2	K562	blood:
3	chr1:180197757..180200322-chr1:180217302..180220148,2	K562	blood:

Variant related genes	Relation type
ENSG00000121454	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12135955	0.90[AMR][1000 genomes]
rs12407014	0.94[ASN][1000 genomes]
rs164982	0.93[ASN][1000 genomes]
rs165257	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs355615	0.91[ASN][1000 genomes]
rs355627	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs355632	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs355633	0.97[ASN][1000 genomes]
rs355636	0.98[ASN][1000 genomes]
rs357069	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs357074	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs357077	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3911335	0.84[ASW][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes]
rs6425617	0.96[ASN][1000 genomes]
rs6673375	0.90[AMR][1000 genomes]
rs7529839	0.91[ASN][1000 genomes]
rs7539240	0.94[ASN][1000 genomes]
rs7539244	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1007590	chr1:180121480-180236452	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS 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
6	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1002133	chr1:180127036-180230081	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv999182	chr1:180127616-180236452	Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv1005512	chr1:180127616-180242659	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1012145	chr1:180132688-180236452	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv1005073	chr1:180152550-180250783	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	diseases
15	nsv535219	chr1:180152550-180250783	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv872575	chr1:180186713-180238243	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
20	nsv1013076	chr1:180214152-180239670	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4652492	QSOX1	cis	parietal	SCAN
rs4652492	RFWD2	cis	cerebellum	SCAN
rs4652492	XPR1	cis	cerebellum	SCAN
rs4652492	RASAL2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180213600-180225800	Weak transcription	Right Atrium	heart
2	chr1:180216400-180221600	Weak transcription	A549	lung
3	chr1:180216600-180221600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:180216800-180218600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:180217000-180218800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:180217000-180218800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:180217000-180218800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:180217000-180221600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:180217200-180218800	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr1:180217400-180218800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:180217400-180219000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:180217400-180222000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:180217600-180219400	Enhancers	HSMMtube	muscle
14	chr1:180217600-180222800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:180218000-180219200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr1:180218200-180218800	Enhancers	HepG2	liver
17	chr1:180218200-180219000	Enhancers	Fetal Lung	lung
18	chr1:180218400-180219000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:180218400-180219200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:180218400-180219200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:180218400-180219600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr1:180218400-180221400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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