Variant report

Variant	rs11577560
Chromosome Location	chr1:120229865-120229866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120229792..120231465-chr1:120324714..120327706,2	MCF-7	breast:
2	chr1:120228899..120230823-chr1:120252883..120254482,3	K562	blood:
3	chr1:120229272..120230952-chr1:120253510..120256383,3	MCF-7	breast:
4	chr1:120229496..120231621-chr1:120254696..120256885,2	K562	blood:

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10218713	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10494229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802132	0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10802133	0.90[ASN][1000 genomes]
rs12121447	0.81[TSI][hapmap]
rs12127451	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12127605	0.86[TSI][hapmap]
rs12144094	1.00[CEU][hapmap]
rs12562763	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565338	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1406917	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1441011	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1853048	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1886736	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2236398	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs3828090	0.83[GIH][hapmap]
rs4659226	0.86[ASN][1000 genomes]
rs55806106	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60466603	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6428840	0.94[ASN][1000 genomes]
rs6683122	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs894079	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs942835	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs9659196	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11577560	PHGDH	cis	parietal	SCAN
rs11577560	HSD3B2	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120222800-120231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:120227000-120231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:120228200-120232200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:120228400-120230000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:120228400-120232400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:120228600-120233000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:120228800-120230200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:120229000-120230200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:120229000-120230200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:120229000-120230400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:120229000-120230400	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:120229000-120230400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:120229000-120230600	Enhancers	Placenta	Placenta
14	chr1:120229000-120230800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:120229000-120230800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:120229000-120232200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:120229000-120232400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:120229200-120230400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:120229200-120230600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:120229200-120231400	Weak transcription	Esophagus	oesophagus
21	chr1:120229400-120230400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:120229400-120230600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:120229400-120231600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:120229600-120230000	Enhancers	NHEK	skin
25	chr1:120229600-120230200	Enhancers	Aorta	Aorta
26	chr1:120229600-120230400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr1:120229600-120230400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:120229600-120230400	Enhancers	Osteobl	bone
29	chr1:120229600-120231400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:120229800-120230000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:120229800-120230000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:120229800-120230000	Flanking Active TSS	HMEC	breast

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