Variant report

Variant	rs1316963
Chromosome Location	chr1:159928711-159928712
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	NFIC	chr1:159928385-159928903	GM12878	blood:	n/a	n/a
2	RUNX3	chr1:159928485-159928871	GM12878	blood:	n/a	n/a
3	ATF2	chr1:159928474-159928886	GM12878	blood:	n/a	n/a
4	RUNX3	chr1:159928577-159929133	GM12878	blood:	n/a	n/a
5	BATF	chr1:159928491-159928876	GM12878	blood:	n/a	n/a
6	IKZF1	chr1:159928530-159929144	GM12878	blood:	n/a	n/a
7	POU2F2	chr1:159928554-159929023	GM12891	blood:	n/a	chr1:159928560-159928570 chr1:159928559-159928573 chr1:159928559-159928572
8	BATF	chr1:159928452-159929056	GM12878	blood:	n/a	n/a
9	IRF4	chr1:159928520-159928854	GM12878	blood:	n/a	n/a

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

Variant related genes	Relation type
LINC01133	TF binding region
SLAMF9	TF binding region
ENSG00000162723	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11265301	0.90[ASN][1000 genomes]
rs2249707	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2789424	0.90[ASN][1000 genomes]
rs2789425	0.81[ASN][1000 genomes]
rs2820555	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2820575	0.81[ASN][1000 genomes]
rs2840584	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs2840585	0.89[EUR][1000 genomes]
rs2840591	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs66496035	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:28 , 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	chr1:159924000-159928800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:159924000-159928800	Weak transcription	Esophagus	oesophagus
5	chr1:159924400-159929200	Weak transcription	Osteobl	bone
6	chr1:159925200-159929600	Weak transcription	NHDF-Ad	bronchial
7	chr1:159925400-159929000	Weak transcription	HMEC	breast
8	chr1:159926400-159928800	Weak transcription	NHEK	skin
9	chr1:159927200-159929600	Enhancers	Fetal Intestine Small	intestine
10	chr1:159927600-159930000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:159927600-159930400	Enhancers	Stomach Mucosa	stomach
12	chr1:159927800-159929000	Enhancers	Gastric	stomach
13	chr1:159927800-159929200	Enhancers	Fetal Intestine Large	intestine
14	chr1:159927800-159929800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:159928000-159928800	Weak transcription	Small Intestine	intestine
16	chr1:159928000-159929000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:159928000-159929000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:159928000-159929000	Weak transcription	Lung	lung
19	chr1:159928000-159929000	Weak transcription	Pancreas	Pancrea
20	chr1:159928000-159929200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:159928000-159931000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:159928000-159931800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:159928000-159941800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:159928200-159931400	Enhancers	K562	blood
25	chr1:159928400-159929600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:159928600-159928800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr1:159928600-159929000	Flanking Active TSS	GM12878-XiMat	blood
28	chr1:159928600-159930400	Enhancers	Placenta	Placenta

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