Variant report

Variant	rs4844815
Chromosome Location	chr1:209529654-209529655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209524634..209532045-chr1:209599866..209610404,18	MCF-7	breast:
2	chr1:209528146..209530754-chr1:209539138..209540797,2	MCF-7	breast:
3	chr1:209527253..209544360-chr1:209599669..209610889,45	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1006316	0.91[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006317	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10494921	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11811038	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs12135550	0.90[JPT][hapmap]
rs1354850	0.94[ASN][1000 genomes]
rs1354852	0.94[ASN][1000 genomes]
rs1354853	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]
rs1395753	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1507331	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1507336	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014320	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17014323	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17014337	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014370	0.91[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014375	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014395	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014396	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1857967	0.84[CHB][hapmap]
rs4844473	0.95[ASN][1000 genomes]
rs4844807	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4844809	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4844820	0.91[ASN][1000 genomes]
rs4844821	0.95[ASN][1000 genomes]
rs55684110	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58017268	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60460414	0.92[ASN][1000 genomes]
rs60534728	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674793	0.94[ASN][1000 genomes]
rs6681466	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74155473	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516864	0.84[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7548184	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
rs4844815	SERTAD4	cis	parietal	SCAN
rs4844815	C1orf97	cis	parietal	SCAN
rs4844815	SOX13	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209525200-209529800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:209526400-209545600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:209527000-209530800	Enhancers	HMEC	breast
4	chr1:209527200-209531000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:209527400-209530400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:209527400-209530800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:209527400-209530800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:209527400-209530800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:209527600-209530800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:209527600-209530800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:209527600-209530800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:209527600-209531000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:209527800-209530200	Weak transcription	HSMMtube	muscle
14	chr1:209528200-209530800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:209528400-209536200	Weak transcription	Esophagus	oesophagus
16	chr1:209528400-209536400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:209529000-209529800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:209529000-209530000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:209529000-209531000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr1:209529200-209529800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:209529200-209530200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:209529200-209530800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:209529400-209529800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:209529400-209531200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:209529600-209529800	Transcr. at gene 5' and 3'	NHEK	skin
26	chr1:209529600-209530000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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