Variant report

Variant	rs56241928
Chromosome Location	chr3:46624467-46624468
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	POLR2A	chr3:46623927-46625241	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:46624374-46624540	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:46624077-46624544	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:46623688-46624637	H1-hESC	embryonic stem cell:	n/a	n/a
5	ATF2	chr3:46624310-46625309	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LRRC2	TF binding region

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1106665	0.86[AMR][1000 genomes]
rs17287770	0.82[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr3:46608400-46625400	Weak transcription	Right Atrium	heart
2	chr3:46616800-46626600	Weak transcription	Pancreas	Pancrea
3	chr3:46618800-46624600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:46620400-46624600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:46621000-46627200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:46621200-46626200	Weak transcription	Dnd41	blood
7	chr3:46622400-46626600	Weak transcription	Colonic Mucosa	Colon
8	chr3:46622600-46626200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:46622600-46626400	Weak transcription	Stomach Mucosa	stomach
10	chr3:46622600-46626800	Weak transcription	Gastric	stomach
11	chr3:46622600-46626800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:46622600-46626800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:46622800-46625400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:46622800-46627200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr3:46622800-46627400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:46623000-46627800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:46623400-46627800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:46623800-46625200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
19	chr3:46623800-46625600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:46623800-46626800	Enhancers	HepG2	liver
21	chr3:46624000-46624600	Genic enhancers	H9 Cell Line	embryonic stem cell
22	chr3:46624000-46625200	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:46624000-46627200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:46624000-46628800	Enhancers	Liver	Liver
25	chr3:46624400-46626200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:46624400-46628000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:46624400-46628800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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