Variant report

Variant	rs56188400
Chromosome Location	chr3:46623292-46623293
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	POLR2A	chr3:46623176-46623312	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LRRC2	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs2280408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280409	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280410	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28617572	0.83[ASN][1000 genomes]
rs28687398	0.80[ASN][1000 genomes]
rs3189859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806704	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312690	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55649212	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55693118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55736632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763532	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55923987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55955974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55957516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56008703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56163098	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs56168669	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs56197743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56394040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56398705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56695799	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58177689	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58551379	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs58572135	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59673973	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59836693	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61739313	1.00[AFR][1000 genomes]
rs73069984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73069987	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73069989	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73069992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73069996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73069997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73071917	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73071919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73071930	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73071938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73072002	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073742	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73073744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73075515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73075519	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075524	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73075528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075540	0.83[AMR][1000 genomes]
rs73075543	0.83[AMR][1000 genomes]
rs73075564	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs73075571	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs73077539	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73077544	0.84[AMR][1000 genomes]
rs73077583	1.00[AFR][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	chr3:46620600-46623400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
6	chr3:46621000-46627200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:46621200-46626200	Weak transcription	Dnd41	blood
8	chr3:46621400-46624000	Weak transcription	Liver	Liver
9	chr3:46621600-46624000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:46622400-46626600	Weak transcription	Colonic Mucosa	Colon
11	chr3:46622600-46623800	Weak transcription	HepG2	liver
12	chr3:46622600-46626200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:46622600-46626400	Weak transcription	Stomach Mucosa	stomach
14	chr3:46622600-46626800	Weak transcription	Gastric	stomach
15	chr3:46622600-46626800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:46622600-46626800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:46622800-46623400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:46622800-46623800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:46622800-46623800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:46622800-46623800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:46622800-46624000	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr3:46622800-46624000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:46622800-46624000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:46622800-46625400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:46622800-46627200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr3:46622800-46627400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:46623000-46627800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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