Variant report

Variant	rs28919894
Chromosome Location	chr5:42807753-42807754
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	HEY1	chr5:42805975-42809968	HepG2	liver:	n/a	n/a
2	NFIC	chr5:42807733-42808685	HepG2	liver:	n/a	n/a
3	MYBL2	chr5:42807377-42809776	HepG2	liver:	n/a	n/a
4	MBD4	chr5:42807663-42808493	HepG2	liver:	n/a	n/a
5	HEY1	chr5:42807644-42808034	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:42805758-42812555	HepG2	liver:	n/a	n/a
7	MBD4	chr5:42804512-42808794	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:42807619-42808796	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:42797012-42808716	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:42798272-42812268	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42804005..42807994-chr5:42809581..42813463,4	K562	blood:

Variant related genes	Relation type
SEPP1	TF binding region
ENSG00000250722	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10041130	0.88[ASN][1000 genomes]
rs10941583	0.82[ASN][1000 genomes]
rs12652476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12654861	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12656017	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12658099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12658163	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12659225	0.87[ASN][1000 genomes]
rs1423655	0.91[ASN][1000 genomes]
rs16872680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872694	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16872762	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872779	0.87[ASN][1000 genomes]
rs16872791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16872825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16872830	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872832	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17839373	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17839374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs230808	0.91[ASN][1000 genomes]
rs230809	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs230811	0.94[ASN][1000 genomes]
rs2548719	0.92[ASN][1000 genomes]
rs28918068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28919901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28919903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28943887	1.00[EUR][1000 genomes]
rs28943888	1.00[EUR][1000 genomes]
rs2910854	0.91[ASN][1000 genomes]
rs2910860	0.91[ASN][1000 genomes]
rs2910863	0.91[ASN][1000 genomes]
rs2910866	0.91[ASN][1000 genomes]
rs2910879	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972752	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972764	0.90[ASN][1000 genomes]
rs2972768	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972769	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972782	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972995	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973004	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973008	0.86[ASN][1000 genomes]
rs2973009	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2973016	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2973019	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2973030	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34319505	1.00[EUR][1000 genomes]
rs34382565	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35389780	1.00[EUR][1000 genomes]
rs35436563	1.00[EUR][1000 genomes]
rs35604733	0.90[ASN][1000 genomes]
rs4376276	0.83[ASN][1000 genomes]
rs4637559	0.83[ASN][1000 genomes]
rs6182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
14	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	309 gene(s)	inside rSNPs	diseases
15	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42789600-42813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:42791400-42811200	Weak transcription	Fetal Thymus	thymus
3	chr5:42795600-42810200	Weak transcription	Thymus	Thymus
4	chr5:42797000-42810600	Weak transcription	Esophagus	oesophagus
5	chr5:42797400-42810800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:42797600-42808200	Weak transcription	HSMM	muscle
7	chr5:42797800-42809200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:42798200-42808400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:42798200-42811200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:42798600-42808200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:42799000-42811600	Weak transcription	HSMMtube	muscle
12	chr5:42799400-42808200	Weak transcription	Colonic Mucosa	Colon
13	chr5:42799600-42811400	Weak transcription	Fetal Brain Female	brain
14	chr5:42799600-42812000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:42799800-42808200	Strong transcription	Placenta	Placenta
16	chr5:42799800-42808400	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:42800000-42808200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:42800000-42809400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:42800600-42808000	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:42800600-42811200	Weak transcription	Small Intestine	intestine
21	chr5:42800800-42808200	Weak transcription	Stomach Mucosa	stomach
22	chr5:42802000-42809000	Weak transcription	Right Ventricle	heart
23	chr5:42802000-42809600	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:42802000-42810200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:42802000-42810200	Weak transcription	Brain Germinal Matrix	brain
26	chr5:42802000-42810600	Weak transcription	Aorta	Aorta
27	chr5:42802000-42810600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:42802000-42810600	Weak transcription	Gastric	stomach
29	chr5:42802000-42810600	Weak transcription	Lung	lung
30	chr5:42802000-42811000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:42802000-42811200	Weak transcription	Spleen	Spleen
32	chr5:42802200-42810200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:42802400-42808200	Weak transcription	Psoas Muscle	Psoas
34	chr5:42802400-42810600	Weak transcription	Pancreas	Pancrea
35	chr5:42802400-42810800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:42803800-42810800	Weak transcription	Fetal Brain Male	brain
37	chr5:42804000-42807800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:42804600-42809400	Weak transcription	Fetal Stomach	stomach
39	chr5:42804800-42808000	Genic enhancers	Brain Hippocampus Middle	brain
40	chr5:42804800-42811200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:42806400-42807800	Weak transcription	Brain Angular Gyrus	brain
42	chr5:42806400-42807800	Strong transcription	Fetal Lung	lung
43	chr5:42806400-42808000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:42806600-42807800	Weak transcription	Osteobl	bone
45	chr5:42806800-42808000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr5:42806800-42808200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:42806800-42808200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:42806800-42808200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr5:42806800-42808200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:42806800-42808200	Weak transcription	Left Ventricle	heart

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