Variant report

Variant	rs1354853
Chromosome Location	chr1:209557991-209557992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:209393308..209395102-chr1:209556912..209559448,2	MCF-7	breast:
2	chr1:209555303..209558478-chr1:209558595..209562675,4	MCF-7	breast:
3	chr1:209555854..209558592-chr1:209584586..209586209,2	MCF-7	breast:
4	chr1:209555442..209558217-chr1:209587307..209589261,2	MCF-7	breast:
5	chr1:209554903..209565803-chr1:209600283..209609508,22	MCF-7	breast:
6	chr1:209557688..209559993-chr1:209600504..209603196,4	MCF-7	breast:
7	chr1:209556562..209561769-chr1:209603992..209608152,7	MCF-7	breast:
8	chr1:209555771..209558011-chr1:209570571..209573206,2	MCF-7	breast:
9	chr1:209557001..209559198-chr1:209583129..209584738,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1006316	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006317	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11811038	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs12135550	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs12142844	0.82[AMR][1000 genomes]
rs12142846	0.89[MEX][hapmap]
rs1354850	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354851	0.88[MEX][hapmap]
rs1354852	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507331	0.88[ASN][1000 genomes]
rs1507335	0.86[LWK][hapmap];0.80[MKK][hapmap];0.94[YRI][hapmap]
rs1507336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014320	0.89[ASN][1000 genomes]
rs17014323	0.89[ASN][1000 genomes]
rs17014337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17014370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17014375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1857967	0.92[CHB][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs4844473	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4844807	0.89[ASN][1000 genomes]
rs4844809	0.89[ASN][1000 genomes]
rs4844815	0.91[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs4844820	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844821	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55684110	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58017268	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60460414	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60534728	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674793	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6681466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs74155473	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516757	0.83[ASN][1000 genomes]
rs7516864	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs7548184	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1354853	MDM4	cis	parietal	SCAN
rs1354853	C1orf97	cis	parietal	SCAN
rs1354853	SOX13	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209549800-209560400	Weak transcription	HSMM	muscle
2	chr1:209550200-209560600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:209553200-209568600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:209555200-209558800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:209555200-209561000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:209555400-209558200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:209555400-209559200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:209555400-209559400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:209555400-209559600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:209555400-209560800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:209555400-209561000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:209555600-209564400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:209555800-209565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:209556000-209558000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:209556000-209558400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr1:209556400-209558400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:209556400-209558400	Flanking Active TSS	NHEK	skin
18	chr1:209556400-209559800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:209556600-209558000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:209556600-209558200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:209556600-209558200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:209556600-209560800	Weak transcription	Esophagus	oesophagus
23	chr1:209556800-209558200	Flanking Active TSS	HMEC	breast
24	chr1:209556800-209560800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:209557000-209560600	Weak transcription	Placenta	Placenta
26	chr1:209557000-209560800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:209557000-209560800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:209557200-209561600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:209557400-209560800	Weak transcription	Osteobl	bone
30	chr1:209557600-209559000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:209557800-209558000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:209557800-209561200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr1:209557800-209565200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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