Variant report

Variant	rs3792839
Chromosome Location	chr5:146783827-146783828
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	USF2	chr5:146783795-146784147	Hela-S3	cervix:	n/a	n/a
2	FOSL2	chr5:146783528-146784401	SK-N-SH	brain:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
3	SMC3	chr5:146783601-146783915	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr5:146783582-146784146	MCF10A-Er-Src	breast:	n/a	chr5:146783748-146783757 chr5:146783749-146783758
5	POLR2A	chr5:146783466-146784263	U87	brain:	n/a	n/a
6	RCOR1	chr5:146783647-146784193	Hela-S3	cervix:	n/a	n/a
7	SPI1	chr5:146783292-146783959	GM12878	blood:	n/a	chr5:146783833-146783840 chr5:146783671-146783684
8	POLR2A	chr5:146783540-146784254	SK-N-SH	brain:	n/a	n/a
9	JUN	chr5:146783187-146784227	HUVEC	blood vessel:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
10	STAT3	chr5:146783700-146784150	Hela-S3	cervix:	n/a	chr5:146783748-146783757 chr5:146783749-146783758
11	PBX3	chr5:146783548-146784325	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr5:146783723-146784241	HUVEC	blood vessel:	n/a	n/a
13	RXRA	chr5:146783504-146784324	SK-N-SH	brain:	n/a	chr5:146783749-146783758 chr5:146783915-146783937 chr5:146783748-146783757
14	STAT3	chr5:146783582-146784136	MCF10A-Er-Src	breast:	n/a	chr5:146783748-146783757 chr5:146783749-146783758
15	JUND	chr5:146783477-146784425	HCT-116	colon:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
16	BATF	chr5:146783780-146784212	GM12878	blood:	n/a	chr5:146784031-146784042
17	NFIC	chr5:146783660-146784310	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:146782857-146784916	IMR90	lung:	n/a	n/a
19	MYC	chr5:146783715-146784208	HUVEC	blood vessel:	n/a	chr5:146783748-146783757
20	JUND	chr5:146782708-146784664	SK-N-SH	brain:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
21	POLR2A	chr5:146783239-146787438	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZKSCAN1	chr5:146783690-146784243	Hela-S3	cervix:	n/a	n/a
23	GTF2F1	chr5:146783665-146784374	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr5:146783316-146784110	MCF10A-Er-Src	breast:	n/a	n/a
25	JUN	chr5:146783572-146784209	Hela-S3	cervix:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
26	EP300	chr5:146783589-146784615	GM12878	blood:	n/a	chr5:146783748-146783757 chr5:146784229-146784243 chr5:146783749-146783758
27	SMC3	chr5:146783728-146784126	GM12878	blood:	n/a	n/a
28	NR3C1	chr5:146783404-146784037	A549	lung:	n/a	chr5:146783524-146783537 chr5:146783651-146783667 chr5:146783828-146783835 chr5:146783651-146783667
29	RAD21	chr5:146783187-146784252	IMR90	lung:	n/a	n/a
30	POLR2A	chr5:146782981-146784367	HUVEC	blood vessel:	n/a	n/a
31	STAT3	chr5:146783584-146784153	MCF10A-Er-Src	breast:	n/a	chr5:146783748-146783757 chr5:146783749-146783758
32	MEF2A	chr5:146783656-146784308	GM12878	blood:	n/a	chr5:146783976-146783990 chr5:146783974-146783995 chr5:146783978-146783989 chr5:146783975-146783991 chr5:146783979-146783988 chr5:146783976-146783991 chr5:146783974-146783995 chr5:146783974-146783995
33	IRF4	chr5:146783804-146784286	GM12878	blood:	n/a	n/a
34	BHLHE40	chr5:146783708-146784651	GM12878	blood:	n/a	n/a
35	FOXM1	chr5:146783794-146784286	GM12878	blood:	n/a	n/a
36	CEBPB	chr5:146783245-146784251	IMR90	lung:	n/a	n/a
37	POLR2A	chr5:146783801-146783833	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr5:146783736-146784254	HCT-116	colon:	n/a	n/a
39	FOSL2	chr5:146783498-146784290	A549	lung:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
40	POLR2A	chr5:146783680-146784214	HCT-116	colon:	n/a	n/a
41	STAT3	chr5:146783567-146784164	MCF10A-Er-Src	breast:	n/a	chr5:146783748-146783757 chr5:146783749-146783758
42	JUND	chr5:146783582-146784289	Hela-S3	cervix:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
43	MAFK	chr5:146783679-146784180	Hela-S3	cervix:	n/a	n/a
44	JUND	chr5:146783448-146784370	HCT-116	colon:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
45	FOSL1	chr5:146783353-146784418	HCT-116	colon:	n/a	chr5:146783748-146783757 chr5:146783749-146783758 chr5:146783749-146783757 chr5:146783749-146783756
46	YY1	chr5:146783818-146784205	GM12878	blood:	n/a	n/a
47	EBF1	chr5:146783740-146784293	GM12878	blood:	n/a	n/a
48	STAT3	chr5:146783316-146784312	MCF10A-Er-Src	breast:	n/a	chr5:146783474-146783482 chr5:146783748-146783757 chr5:146783749-146783758
49	USF2	chr5:146783823-146784605	GM12878	blood:	n/a	chr5:146784512-146784523
50	IKZF1	chr5:146783689-146784265	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
DPYSL3	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10042298	1.00[CEU][hapmap]
rs10043932	1.00[CEU][hapmap]
rs10045916	1.00[CEU][hapmap]
rs10476887	1.00[CEU][hapmap]
rs10515581	0.81[CHD][hapmap]
rs10515583	0.80[CHB][hapmap]
rs11167989	0.80[CHB][hapmap]
rs11952440	0.81[ASW][hapmap];1.00[CEU][hapmap]
rs11955404	1.00[CEU][hapmap]
rs12514302	0.80[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12515377	0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs12518292	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12653560	0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs12657083	1.00[CEU][hapmap]
rs1432838	0.80[CHB][hapmap]
rs1432852	1.00[CEU][hapmap]
rs1432853	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs1432854	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs1432855	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs1432856	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs1432857	0.93[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs1549915	1.00[CEU][hapmap]
rs17096661	1.00[CEU][hapmap]
rs17106492	0.81[CHD][hapmap]
rs17106572	0.80[CHB][hapmap]
rs17106575	0.80[CHB][hapmap]
rs17106592	0.84[JPT][hapmap]
rs17106679	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs17106682	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs17106683	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs17106686	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs17106688	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs17106689	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17106690	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs17106698	0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs17106701	0.93[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs17106725	1.00[CEU][hapmap]
rs2163767	1.00[CEU][hapmap]
rs2288800	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs2288805	0.93[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs2288809	0.93[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2304043	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2304047	0.94[ASN][1000 genomes]
rs3213857	0.93[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs3749721	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3792837	0.80[CHB][hapmap]
rs3792840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3792841	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3792843	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3792844	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs3792845	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs3792846	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3805533	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3805534	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs3805535	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3805538	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3805539	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs3805540	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs3805542	0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3805543	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs3805544	0.92[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs3805545	0.93[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs3805546	0.93[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs3816012	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6886313	1.00[CEU][hapmap]
rs6891468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs6897123	1.00[CEU][hapmap]
rs7714240	0.80[CHB][hapmap]
rs7737670	1.00[CEU][hapmap]
rs972302	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146762800-146784200	Weak transcription	Colonic Mucosa	Colon
2	chr5:146767800-146796600	Strong transcription	Brain Germinal Matrix	brain
3	chr5:146768000-146784000	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:146769400-146800600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:146769800-146810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:146770000-146800600	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr5:146770200-146784800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:146770200-146805200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:146770200-146810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:146770400-146796600	Strong transcription	Fetal Brain Female	brain
11	chr5:146770400-146800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:146770600-146798200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:146770600-146800400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:146771600-146786600	Weak transcription	Gastric	stomach
15	chr5:146772800-146795600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:146773400-146784000	Weak transcription	Fetal Brain Male	brain
17	chr5:146773600-146788200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:146773600-146800600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:146774000-146799400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:146774200-146796800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:146774600-146784200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:146775400-146797000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:146776200-146796000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:146777600-146796800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:146777600-146800600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr5:146777800-146790400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:146778800-146785000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:146779800-146798400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:146780200-146784600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:146780400-146796800	Weak transcription	Spleen	Spleen
31	chr5:146780600-146784000	Weak transcription	Brain Anterior Caudate	brain
32	chr5:146780800-146796600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr5:146781200-146784200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:146781200-146784200	Weak transcription	Fetal Intestine Small	intestine
35	chr5:146781400-146784000	Weak transcription	Fetal Intestine Large	intestine
36	chr5:146781400-146784400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:146781400-146784600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:146782400-146784800	Enhancers	Aorta	Aorta
39	chr5:146782400-146784800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr5:146782400-146790600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:146782600-146784200	Enhancers	NH-A	brain
42	chr5:146782600-146784400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:146782600-146784600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:146782600-146785400	Enhancers	HUVEC	blood vessel
45	chr5:146782800-146784000	Flanking Active TSS	NHDF-Ad	bronchial
46	chr5:146782800-146784400	Enhancers	Rectal Smooth Muscle	rectum
47	chr5:146782800-146791800	Enhancers	Fetal Heart	heart
48	chr5:146783000-146784200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:146783000-146785400	Genic enhancers	Fetal Muscle Leg	muscle
50	chr5:146783200-146784000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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