Variant report

Variant	rs11675417
Chromosome Location	chr2:47754445-47754446
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	FOXA1	chr2:47754401-47754688	HepG2	liver:	n/a	n/a
2	FOXA2	chr2:47754358-47754761	A549	lung:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPCAM-3	chr2:47753816-47754943	NONHSAT070583
2	lnc-EPCAM-3	chr2:47753816-47754943	NONHSAT070584

Variant related genes	Relation type
ENSG00000235760	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12612893	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12619323	0.80[ASN][1000 genomes]
rs6751501	0.87[CEU][hapmap];0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs7587143	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv998314	chr2:47720420-47959168	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv817599	chr2:47738456-47961099	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47743600-47778200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:47747800-47755400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:47748800-47755200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:47748800-47755600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:47748800-47757200	Weak transcription	Right Atrium	heart
6	chr2:47748800-47761000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:47748800-47772800	Weak transcription	Gastric	stomach
8	chr2:47749000-47755000	Weak transcription	Brain Angular Gyrus	brain
9	chr2:47749000-47761800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:47749000-47771000	Weak transcription	Ovary	ovary
11	chr2:47749200-47761000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:47749200-47762400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:47749400-47754800	Weak transcription	Fetal Brain Female	brain
14	chr2:47749400-47760000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:47749400-47760600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:47752600-47758000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:47752800-47754800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:47752800-47756200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:47753000-47755600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:47753000-47758600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:47754200-47754800	Strong transcription	Fetal Stomach	stomach

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