Variant report

Variant	rs17024340
Chromosome Location	chr1:120358925-120358926
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	ARID3A	chr1:120358759-120359483	HepG2	liver:	n/a	n/a
2	MYBL2	chr1:120358853-120359562	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:120358921-120359424	HepG2	liver:	n/a	n/a
4	NFIC	chr1:120358724-120359671	HepG2	liver:	n/a	n/a
5	MBD4	chr1:120358924-120359452	HepG2	liver:	n/a	n/a
6	FOXA1	chr1:120358904-120359487	HepG2	liver:	n/a	n/a
7	FOXA1	chr1:120358874-120359469	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120358099..120360727-chr1:144531568..144534050,2	K562	blood:
2	chr1:120333977..120336154-chr1:120357521..120360172,2	MCF-7	breast:

Variant related genes	Relation type
REG4	TF binding region
ENSG00000201699	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10158823	0.92[ASW][hapmap];1.00[MEX][hapmap]
rs10923908	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10923922	1.00[MEX][hapmap]
rs12057495	0.84[ASW][hapmap];1.00[MEX][hapmap]
rs12059465	0.83[YRI][hapmap]
rs12072780	1.00[MEX][hapmap]
rs1341408	0.85[AFR][1000 genomes]
rs17038441	0.87[AMR][1000 genomes]
rs3850867	1.00[MEX][hapmap]
rs6666925	0.83[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv947316	chr1:120355309-120362730	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120356600-120361200	Enhancers	Fetal Intestine Small	intestine
2	chr1:120356800-120359600	Enhancers	Stomach Mucosa	stomach
3	chr1:120356800-120359800	Enhancers	HMEC	breast
4	chr1:120356800-120361000	Enhancers	Fetal Intestine Large	intestine
5	chr1:120356800-120361200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:120357000-120359400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:120357000-120359600	Enhancers	HSMM	muscle
8	chr1:120357000-120359800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:120357000-120359800	Enhancers	NHEK	skin
10	chr1:120357000-120360800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:120357200-120361000	Enhancers	HepG2	liver
12	chr1:120357600-120359600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:120357600-120359600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:120357800-120359400	Enhancers	NH-A	brain
15	chr1:120357800-120359800	Enhancers	K562	blood
16	chr1:120358000-120359000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:120358200-120359600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:120358200-120359600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:120358200-120359600	Enhancers	Osteobl	bone
20	chr1:120358400-120359600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:120358400-120360200	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:120358600-120359000	Weak transcription	Fetal Heart	heart
23	chr1:120358600-120359000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr1:120358600-120359400	Enhancers	NHLF	lung
25	chr1:120358600-120359800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:120358800-120359000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:120358800-120360800	Enhancers	Liver	Liver

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