Variant report

Variant	rs782984
Chromosome Location	chr5:43172896-43172897
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	MAX	chr5:43172875-43173201	NB4	blood:	n/a	chr5:43173036-43173046 chr5:43173048-43173058

Variant related genes	Relation type
ZNF131	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10064003	0.90[JPT][hapmap]
rs10522	0.90[JPT][hapmap]
rs10941604	0.86[JPT][hapmap]
rs10941605	0.86[JPT][hapmap]
rs12518336	0.81[EUR][1000 genomes]
rs12655504	0.88[CEU][hapmap]
rs12697439	0.90[JPT][hapmap]
rs13169690	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs13170208	0.90[JPT][hapmap]
rs1542369	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1574407	0.90[JPT][hapmap]
rs160709	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs1618891	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1624415	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1628981	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1670796	0.88[CEU][hapmap]
rs1690994	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1690997	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs178415	0.92[CHD][hapmap];0.90[JPT][hapmap]
rs2100473	0.86[JPT][hapmap]
rs222060	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs2329995	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs2444779	0.81[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap]
rs2453308	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548350	0.81[JPT][hapmap]
rs2548353	0.86[JPT][hapmap]
rs2548356	0.86[JPT][hapmap];0.84[YRI][hapmap]
rs2603656	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs309909	0.86[JPT][hapmap]
rs309914	0.90[JPT][hapmap]
rs316404	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs316408	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs316413	0.92[CHD][hapmap];0.90[JPT][hapmap]
rs316414	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4092293	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs4092294	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs479996	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4866811	0.88[CEU][hapmap]
rs499436	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511340	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs512040	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512921	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs521649	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs541143	0.80[YRI][hapmap]
rs544402	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555276	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs557076	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs567884	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs574051	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57689195	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs579337	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs579363	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61004923	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61121229	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs643307	0.90[JPT][hapmap]
rs6451660	0.90[JPT][hapmap]
rs6451661	0.90[JPT][hapmap]
rs6451662	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs6879130	0.90[JPT][hapmap]
rs6892422	0.80[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724430	0.86[JPT][hapmap]
rs768441	0.90[JPT][hapmap]
rs7715065	0.86[JPT][hapmap]
rs782971	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782972	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782976	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782977	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782978	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782987	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782989	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782994	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782996	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292862	0.82[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs782984	LOC643977	cis	multi-tissue	Pritchard
rs782984	TTLL7	trans	parietal	SCAN
rs782984	FYB	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43122800-43174200	Weak transcription	Colonic Mucosa	Colon
2	chr5:43124000-43183000	Weak transcription	Small Intestine	intestine
3	chr5:43127600-43178000	Strong transcription	Dnd41	blood
4	chr5:43143400-43178200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:43155200-43177200	Weak transcription	Fetal Heart	heart
6	chr5:43155800-43176600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:43156000-43178200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:43156200-43174600	Weak transcription	Right Ventricle	heart
9	chr5:43156600-43191200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:43156800-43174200	Weak transcription	Gastric	stomach
11	chr5:43156800-43177600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:43157000-43173400	Weak transcription	Brain Substantia Nigra	brain
13	chr5:43157000-43178400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:43161400-43176800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:43162000-43173000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:43162000-43173400	Weak transcription	HSMMtube	muscle
17	chr5:43162000-43174000	Weak transcription	NHLF	lung
18	chr5:43162000-43174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:43162000-43174600	Weak transcription	Esophagus	oesophagus
20	chr5:43162000-43174600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:43162000-43176600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:43162000-43191600	Weak transcription	Fetal Brain Male	brain
23	chr5:43162200-43173400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:43162200-43173600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:43162600-43174600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:43163400-43175800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:43163600-43173400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:43163800-43174600	Weak transcription	Pancreas	Pancrea
29	chr5:43163800-43174600	Weak transcription	Spleen	Spleen
30	chr5:43163800-43174800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:43163800-43191800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:43164200-43174600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:43164400-43173400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:43164400-43191200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:43164600-43173200	Weak transcription	Brain Germinal Matrix	brain
36	chr5:43164600-43174400	Weak transcription	Brain Angular Gyrus	brain
37	chr5:43164600-43174400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:43165000-43173400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:43165000-43174400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:43165000-43191200	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:43165200-43174200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr5:43165600-43174200	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:43165800-43174600	Weak transcription	Psoas Muscle	Psoas
44	chr5:43166000-43173400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:43166200-43173400	Weak transcription	HMEC	breast
46	chr5:43166400-43173400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:43166400-43173400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:43166400-43173400	Weak transcription	Fetal Kidney	kidney
49	chr5:43166800-43175400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:43167600-43175800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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