Variant report

Variant	rs16872791
Chromosome Location	chr5:42809500-42809501
allele	A/G
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	NFIC	chr5:42809384-42809785	HepG2	liver:	n/a	n/a
2	HEY1	chr5:42805975-42809968	HepG2	liver:	n/a	n/a
3	HEY1	chr5:42809025-42809734	HepG2	liver:	n/a	n/a
4	MYBL2	chr5:42807377-42809776	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:42809068-42809638	HepG2	liver:	n/a	n/a
6	RCOR1	chr5:42809433-42809619	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:42809195-42809848	HepG2	liver:	n/a	n/a
8	MBD4	chr5:42809006-42810591	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:42805758-42812555	HepG2	liver:	n/a	n/a
10	MBD4	chr5:42808938-42809646	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:42808118-42809598	HepG2	liver:	n/a	n/a
12	POLR2A	chr5:42809471-42809616	HepG2	liver:	n/a	n/a
13	POLR2A	chr5:42798272-42812268	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:42807877-42809854	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42808126..42809697-chr5:42810037..42813024,2	K562	blood:

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

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10038285	0.89[JPT][hapmap]
rs10038477	0.90[JPT][hapmap]
rs10041130	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10044169	0.90[JPT][hapmap]
rs10061833	1.00[JPT][hapmap]
rs10077296	0.90[JPT][hapmap]
rs10941583	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12652476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12654861	1.00[CHB][hapmap];1.00[JPT][hapmap];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[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16872680	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16872694	1.00[CHB][hapmap];1.00[JPT][hapmap];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[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872777	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872779	0.81[CHB][hapmap];0.88[JPT][hapmap];0.87[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]
rs28919894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28919901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28919903	1.00[CHB][hapmap];1.00[JPT][hapmap];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[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2910863	0.91[ASN][1000 genomes]
rs2910866	0.91[ASN][1000 genomes]
rs2910878	0.90[JPT][hapmap]
rs2910879	1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs2972780	0.89[JPT][hapmap]
rs2972782	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972991	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972995	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973004	1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs4146624	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs4242119	0.89[JPT][hapmap]
rs4273617	0.89[JPT][hapmap]
rs4376276	0.83[ASN][1000 genomes]
rs4547964	0.84[JPT][hapmap]
rs4637559	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4866948	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs6179	0.89[JPT][hapmap]
rs6182	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6184	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7703289	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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
16	esv3385871	chr5:42808978-42809551	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 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	chr5:42798200-42811200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:42799000-42811600	Weak transcription	HSMMtube	muscle
8	chr5:42799600-42811400	Weak transcription	Fetal Brain Female	brain
9	chr5:42799600-42812000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:42800600-42811200	Weak transcription	Small Intestine	intestine
11	chr5:42802000-42809600	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:42802000-42810200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:42802000-42810200	Weak transcription	Brain Germinal Matrix	brain
14	chr5:42802000-42810600	Weak transcription	Aorta	Aorta
15	chr5:42802000-42810600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:42802000-42810600	Weak transcription	Gastric	stomach
17	chr5:42802000-42810600	Weak transcription	Lung	lung
18	chr5:42802000-42811000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:42802000-42811200	Weak transcription	Spleen	Spleen
20	chr5:42802200-42810200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:42802400-42810600	Weak transcription	Pancreas	Pancrea
22	chr5:42802400-42810800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:42803800-42810800	Weak transcription	Fetal Brain Male	brain
24	chr5:42804800-42811200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:42807200-42810200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:42807200-42810200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:42807200-42810800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:42807600-42809600	Transcr. at gene 5' and 3'	HepG2	liver
29	chr5:42807600-42812600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr5:42807800-42809800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:42807800-42812800	Active TSS	Right Atrium	heart
32	chr5:42808000-42809600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:42808000-42812600	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr5:42808200-42810400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:42808200-42811000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:42808200-42812200	Active TSS	Duodenum Mucosa	Duodenum
37	chr5:42808200-42812600	Active TSS	Colonic Mucosa	Colon
38	chr5:42808400-42810200	Weak transcription	NHDF-Ad	bronchial
39	chr5:42808400-42810800	Weak transcription	Osteobl	bone
40	chr5:42808400-42811600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:42808400-42812400	Active TSS	Brain Cingulate Gyrus	brain
42	chr5:42808400-42812400	Active TSS	Brain Substantia Nigra	brain
43	chr5:42808400-42812400	Active TSS	Placenta	Placenta
44	chr5:42808400-42812600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:42808400-42812600	Active TSS	Ovary	ovary
46	chr5:42808400-42812600	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr5:42808600-42810800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:42808600-42810800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:42808600-42810800	Weak transcription	Stomach Mucosa	stomach
50	chr5:42808600-42811400	Active TSS	Rectal Mucosa Donor 31	rectum

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