Variant report

Variant	rs71628163
Chromosome Location	chr1:159930635-159930636
allele	C/T
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	chr1:159930362-159931187	MCF10A-Er-Src	breast:	n/a	chr1:159930983-159930992
2	MYC	chr1:159930456-159931147	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr1:159930423-159930767	K562	blood:	n/a	n/a
4	STAT3	chr1:159930544-159931125	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:159930451-159931087	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:159930399-159931180	MCF10A-Er-Src	breast:	n/a	chr1:159930983-159930992
7	FOS	chr1:159930386-159931090	MCF10A-Er-Src	breast:	n/a	chr1:159930983-159930992
8	MAX	chr1:159930585-159930731	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr1:159930419-159931081	MCF10A-Er-Src	breast:	n/a	n/a
10	GATA1	chr1:159930531-159931402	PBDE	blood:	n/a	n/a
11	STAT3	chr1:159930444-159931177	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr1:159930576-159931175	IMR90	lung:	n/a	chr1:159930982-159930990
13	MAX	chr1:159930449-159931164	Hela-S3	cervix:	n/a	n/a
14	FOS	chr1:159930369-159931123	MCF10A-Er-Src	breast:	n/a	chr1:159930983-159930992
15	MYC	chr1:159930465-159931074	MCF10A-Er-Src	breast:	n/a	n/a
16	SP1	chr1:159930366-159931157	HCT-116	colon:	n/a	chr1:159930980-159931001

No.	Distal block	Cell Line	Cell type
1	chr1:159925103..159927154-chr1:159928753..159930871,2	MCF-7	breast:
2	chr1:159914809..159917137-chr1:159930388..159932667,2	K562	blood:
3	chr1:159913973..159917644-chr1:159927852..159934070,11	MCF-7	breast:

Variant related genes	Relation type
LINC01133	TF binding region
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12065741	1.00[ASN][1000 genomes]
rs12144158	0.87[ASN][1000 genomes]
rs12732517	1.00[ASN][1000 genomes]
rs12740563	0.87[ASN][1000 genomes]
rs12759403	0.87[ASN][1000 genomes]
rs1344028	0.87[ASN][1000 genomes]
rs2789426	0.87[ASN][1000 genomes]
rs2840590	1.00[ASN][1000 genomes]
rs34128710	0.87[ASN][1000 genomes]
rs34401812	0.87[ASN][1000 genomes]
rs34702040	0.87[ASN][1000 genomes]
rs35541552	0.87[ASN][1000 genomes]
rs35622571	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35769623	0.87[ASN][1000 genomes]
rs41265747	1.00[ASN][1000 genomes]
rs57616807	0.89[ASN][1000 genomes]
rs58872353	1.00[ASN][1000 genomes]
rs59673346	1.00[ASN][1000 genomes]
rs60537025	1.00[ASN][1000 genomes]
rs61734538	1.00[ASN][1000 genomes]
rs71628159	0.87[ASN][1000 genomes]
rs71628160	1.00[ASN][1000 genomes]
rs71628162	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv548055	chr1:159918418-159940000	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520773	chr1:159922959-159935569	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159928000-159931000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:159928000-159931800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:159928000-159941800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:159928200-159931400	Enhancers	K562	blood
5	chr1:159928800-159931400	Enhancers	Esophagus	oesophagus
6	chr1:159929000-159931000	Weak transcription	Gastric	stomach
7	chr1:159929000-159931000	Enhancers	HMEC	breast
8	chr1:159929000-159931600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:159929400-159934000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:159930200-159931000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:159930200-159931000	Enhancers	Fetal Intestine Large	intestine
12	chr1:159930200-159931200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:159930400-159930800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:159930400-159931000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:159930400-159931000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:159930400-159931000	Weak transcription	Stomach Mucosa	stomach
17	chr1:159930600-159930800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:159930600-159930800	Enhancers	Right Atrium	heart
19	chr1:159930600-159930800	Active TSS	Osteobl	bone
20	chr1:159930600-159931000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:159930600-159931000	Enhancers	Fetal Intestine Small	intestine
22	chr1:159930600-159931000	Enhancers	Rectal Smooth Muscle	rectum
23	chr1:159930600-159931000	Enhancers	HSMM	muscle
24	chr1:159930600-159931000	Enhancers	NHDF-Ad	bronchial
25	chr1:159930600-159931000	Enhancers	NHLF	lung
26	chr1:159930600-159931200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr1:159930600-159931600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:159930600-159931600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:159930600-159931600	Enhancers	Ovary	ovary
30	chr1:159930600-159932200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:159930600-159932400	Active TSS	NHEK	skin

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