Variant report

Variant	rs4559524
Chromosome Location	chr1:161045128-161045129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:161044493-161045134	MCF10A-Er-Src	breast:	n/a	chr1:161044642-161044651
2	MYC	chr1:161044483-161045214	MCF10A-Er-Src	breast:	n/a	chr1:161044678-161044688
3	FOS	chr1:161044502-161045134	MCF10A-Er-Src	breast:	n/a	chr1:161044642-161044651
4	MYC	chr1:161044507-161045216	MCF10A-Er-Src	breast:	n/a	chr1:161044678-161044688

No.	Distal block	Cell Line	Cell type
1	chr1:161045029..161046710-chr1:161057509..161060408,2	K562	blood:
2	chr1:161015334..161017315-chr1:161043865..161045880,2	MCF-7	breast:
3	chr1:161040956..161045180-chr1:161134527..161136918,3	MCF-7	breast:
4	chr1:161006354..161009878-chr1:161042497..161045575,4	MCF-7	breast:

Variant related genes	Relation type
PVRL4	TF binding region
ENSG00000215845	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000143224	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000143217	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10797092	0.90[MKK][hapmap]
rs10908822	0.89[AFR][1000 genomes]
rs11265547	0.89[AFR][1000 genomes]
rs11265548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs11577230	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11590097	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv947135	chr1:161041002-161050287	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4559524	TSTD1	cis	Nerve Tibial	GTEx
rs4559524	TSTD1	cis	Artery Tibial	GTEx
rs4559524	TSTD1	cis	Adipose Subcutaneous	GTEx
rs4559524	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161030000-161046200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:161039600-161049000	Weak transcription	Lung	lung
3	chr1:161039600-161066800	Weak transcription	Right Atrium	heart
4	chr1:161039800-161049000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:161039800-161052600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:161039800-161053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:161040200-161052600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:161040200-161052800	Weak transcription	Colonic Mucosa	Colon
9	chr1:161040800-161046800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:161042400-161049400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr1:161043000-161046800	Enhancers	HMEC	breast
12	chr1:161043400-161047000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:161043600-161045400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:161043600-161052800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:161043800-161050000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:161043800-161052200	Weak transcription	Spleen	Spleen
17	chr1:161044000-161046200	Genic enhancers	Placenta	Placenta
18	chr1:161044200-161047200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:161044200-161047600	Strong transcription	Pancreas	Pancrea
20	chr1:161044800-161045400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:161045000-161045400	Enhancers	NHEK	skin
22	chr1:161045000-161046000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:161045000-161046000	Weak transcription	Esophagus	oesophagus
24	chr1:161045000-161047200	Weak transcription	Gastric	stomach
25	chr1:161045000-161047200	Weak transcription	Stomach Mucosa	stomach
26	chr1:161045000-161047200	Weak transcription	HepG2	liver
27	chr1:161045000-161049000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:161045000-161050400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:161045000-161050800	Weak transcription	HSMM	muscle
30	chr1:161045000-161052400	Weak transcription	A549	lung
31	chr1:161045000-161053200	Weak transcription	Duodenum Mucosa	Duodenum

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