Variant report

Variant	rs12732517
Chromosome Location	chr1:159929140-159929141
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:159929137-159929723	ECC-1	luminal epithelium:	n/a	n/a
2	GATA3	chr1:159929086-159929749	T-47D	breast:	n/a	chr1:159929660-159929671 chr1:159929715-159929725
3	STAT3	chr1:159929086-159929217	MCF10A-Er-Src	breast:	n/a	n/a
4	IKZF1	chr1:159928530-159929144	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:159893947..159895991-chr1:159928260..159930233,2	MCF-7	breast:
2	chr1:159925103..159927154-chr1:159928753..159930871,2	MCF-7	breast:
3	chr1:159926244..159929298-chr1:159931208..159934136,4	K562	blood:
4	chr1:159914406..159916851-chr1:159926521..159929440,2	MCF-7	breast:
5	chr1:159922806..159924393-chr1:159927902..159929423,2	MCF-7	breast:
6	chr1:159894586..159896290-chr1:159926599..159929253,2	K562	blood:
7	chr1:159913973..159917644-chr1:159927852..159934070,11	MCF-7	breast:

No data

Variant related genes	Relation type
LINC01133	TF binding region
ENSG00000158710	Chromatin interaction
ENSG00000162723	Chromatin interaction
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12065741	1.00[ASN][1000 genomes]
rs12144158	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12740563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12759403	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1344028	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2789426	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2840590	1.00[ASN][1000 genomes]
rs34128710	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34401812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34702040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35541552	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35622571	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35769623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36082532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][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]
rs71628158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71628159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71628160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628161	1.00[AMR][1000 genomes]
rs71628162	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71628163	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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
2	chr1:159919800-159930400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:159924400-159929200	Weak transcription	Osteobl	bone
4	chr1:159925200-159929600	Weak transcription	NHDF-Ad	bronchial
5	chr1:159927200-159929600	Enhancers	Fetal Intestine Small	intestine
6	chr1:159927600-159930000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:159927600-159930400	Enhancers	Stomach Mucosa	stomach
8	chr1:159927800-159929200	Enhancers	Fetal Intestine Large	intestine
9	chr1:159927800-159929800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:159928000-159929200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:159928000-159931000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:159928000-159931800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:159928000-159941800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:159928200-159931400	Enhancers	K562	blood
15	chr1:159928400-159929600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:159928600-159930400	Enhancers	Placenta	Placenta
17	chr1:159928800-159930200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:159928800-159930200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:159928800-159930600	Enhancers	NHEK	skin
20	chr1:159928800-159931400	Enhancers	Esophagus	oesophagus
21	chr1:159929000-159929200	Weak transcription	Small Intestine	intestine
22	chr1:159929000-159929400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:159929000-159929400	Enhancers	Lung	lung
24	chr1:159929000-159929400	Enhancers	Pancreas	Pancrea
25	chr1:159929000-159929600	Enhancers	GM12878-XiMat	blood
26	chr1:159929000-159929800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:159929000-159929800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:159929000-159931000	Weak transcription	Gastric	stomach
29	chr1:159929000-159931000	Enhancers	HMEC	breast
30	chr1:159929000-159931600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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