Variant report

Variant	rs2090035
Chromosome Location	chr2:20372270-20372271
allele	G/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	MYC	chr2:20372045-20372316	MCF10A-Er-Src	breast:	n/a	n/a
2	BHLHE40	chr2:20372252-20372519	HepG2	liver:	n/a	chr2:20372393-20372409
3	FOXA1	chr2:20372236-20372677	HepG2	liver:	n/a	n/a
4	FOXA1	chr2:20372211-20372700	HepG2	liver:	n/a	n/a
5	EP300	chr2:20372238-20372667	HepG2	liver:	n/a	n/a
6	EP300	chr2:20372226-20372647	HepG2	liver:	n/a	n/a
7	FOXA1	chr2:20372233-20372675	HepG2	liver:	n/a	n/a
8	TCF7L2	chr2:20372126-20372864	HepG2	liver:	n/a	chr2:20372428-20372437
9	POLR2A	chr2:20372261-20372513	K562	blood:	n/a	n/a
10	YY1	chr2:20371966-20372534	HepG2	liver:	n/a	n/a
11	HDAC2	chr2:20372121-20372568	HepG2	liver:	n/a	chr2:20372505-20372519 chr2:20372506-20372520

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20359744..20361850-chr2:20371412..20373041,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL140P	TF binding region
RNU6-961P	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11894335	0.89[AMR][1000 genomes]
rs13428318	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs2137718	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907869	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs907872	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv997958	chr2:20349343-20386339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv999131	chr2:20350751-20377607	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv998067	chr2:20350751-20386339	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20363800-20374000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:20366800-20372600	Enhancers	Placenta	Placenta
3	chr2:20367200-20376600	Weak transcription	Stomach Mucosa	stomach
4	chr2:20367800-20383600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:20369000-20374400	Enhancers	Esophagus	oesophagus
6	chr2:20369600-20377800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:20369800-20374200	Enhancers	Liver	Liver
8	chr2:20370000-20373200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:20370200-20379800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:20370800-20372400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:20370800-20372400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:20371000-20372600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:20371200-20372400	Enhancers	Fetal Stomach	stomach
14	chr2:20371200-20373000	Enhancers	Fetal Lung	lung
15	chr2:20371200-20373600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:20371200-20373800	Enhancers	HMEC	breast
17	chr2:20371400-20372400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr2:20371600-20372400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr2:20371600-20373000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:20371600-20380800	Weak transcription	Lung	lung
21	chr2:20371800-20373200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:20371800-20375200	Weak transcription	Right Atrium	heart
23	chr2:20372000-20372400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:20372000-20372400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:20372000-20372600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:20372000-20372600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:20372000-20372800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:20372000-20372800	Flanking Active TSS	HepG2	liver
29	chr2:20372200-20372400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:20372200-20372400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:20372200-20372400	Enhancers	Brain Germinal Matrix	brain
32	chr2:20372200-20372600	Enhancers	GM12878-XiMat	blood
33	chr2:20372200-20372600	Flanking Active TSS	NHEK	skin
34	chr2:20372200-20372800	Weak transcription	Fetal Kidney	kidney

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