Variant report

Variant	rs3792846
Chromosome Location	chr5:146790491-146790492
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	EP300	chr5:146789636-146791973	SK-N-SH	brain:	n/a	chr5:146790101-146790108 chr5:146790535-146790544
2	GATA3	chr5:146789973-146790614	T-47D	breast:	n/a	chr5:146790536-146790546
3	EP300	chr5:146790006-146790521	T-47D	breast:	n/a	chr5:146790101-146790108
4	GATA3	chr5:146789971-146790638	SH-SY5Y	brain:	n/a	chr5:146790536-146790546
5	GATA2	chr5:146790191-146791744	SH-SY5Y	brain:	n/a	chr5:146790536-146790546
6	EP300	chr5:146790231-146790556	SK-N-SH_RA	brain:	n/a	chr5:146790535-146790544
7	GATA3	chr5:146790055-146790601	T-47D	breast:	n/a	chr5:146790536-146790546

Variant related genes	Relation type
DPYSL3	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10515581	0.81[CHD][hapmap]
rs10515583	0.80[CHB][hapmap]
rs11167989	0.80[CHB][hapmap]
rs12514302	0.80[CHB][hapmap];0.85[ASN][1000 genomes]
rs12515377	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12518292	0.89[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs12653560	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12657809	1.00[EUR][1000 genomes]
rs1432838	0.80[CHB][hapmap]
rs1432853	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432854	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432857	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106492	0.81[CHD][hapmap]
rs17106572	0.80[CHB][hapmap]
rs17106575	0.80[CHB][hapmap]
rs17106679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106688	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106689	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17106698	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106701	0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106709	0.86[CHD][hapmap];1.00[EUR][1000 genomes]
rs17106713	1.00[EUR][1000 genomes]
rs17106716	1.00[EUR][1000 genomes]
rs2288800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288805	0.93[CHB][hapmap];0.91[ASN][1000 genomes]
rs2288809	0.93[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs2304043	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs2304047	0.91[ASN][1000 genomes]
rs3213857	0.93[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs3749721	0.80[CHB][hapmap]
rs3792837	0.80[CHB][hapmap]
rs3792839	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3792840	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs3792841	0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3792843	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3792844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805533	0.80[CHB][hapmap]
rs3805534	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs3805535	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs3805538	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3805539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805542	0.82[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3805543	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805544	0.92[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805545	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805546	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816012	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs6891468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897123	1.00[EUR][1000 genomes]
rs7714240	0.80[CHB][hapmap]
rs972302	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3792846	DPYSL3	cis	multi-tissue	Pritchard

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146767800-146796600	Strong transcription	Brain Germinal Matrix	brain
2	chr5:146769400-146800600	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:146769800-146810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:146770000-146800600	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr5:146770200-146805200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:146770200-146810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:146770400-146796600	Strong transcription	Fetal Brain Female	brain
8	chr5:146770400-146800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:146770600-146798200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:146770600-146800400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:146772800-146795600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:146773600-146800600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:146774000-146799400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:146774200-146796800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:146775400-146797000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:146776200-146796000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr5:146777600-146796800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:146777600-146800600	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr5:146779800-146798400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:146780400-146796800	Weak transcription	Spleen	Spleen
21	chr5:146780800-146796600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:146782400-146790600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:146782800-146791800	Enhancers	Fetal Heart	heart
24	chr5:146783400-146796200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:146783400-146800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:146784400-146791200	Weak transcription	Brain Anterior Caudate	brain
27	chr5:146784400-146792600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:146784400-146797000	Weak transcription	Brain Angular Gyrus	brain
29	chr5:146784600-146790600	Weak transcription	Placenta	Placenta
30	chr5:146784600-146794400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:146784600-146796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:146784600-146796800	Weak transcription	Colonic Mucosa	Colon
33	chr5:146784600-146797000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:146784600-146797000	Weak transcription	Esophagus	oesophagus
35	chr5:146784600-146800400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:146784800-146795200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:146784800-146807400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:146785000-146795400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:146785400-146790600	Weak transcription	Lung	lung
40	chr5:146785400-146808800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:146786800-146790600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr5:146786800-146790600	Weak transcription	Left Ventricle	heart
43	chr5:146786800-146790600	Weak transcription	Psoas Muscle	Psoas
44	chr5:146787000-146792600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:146787000-146792800	Weak transcription	NHDF-Ad	bronchial
46	chr5:146787000-146798800	Weak transcription	Right Ventricle	heart
47	chr5:146787200-146790800	Weak transcription	HSMM	muscle
48	chr5:146787200-146791600	Weak transcription	Aorta	Aorta
49	chr5:146787200-146795400	Genic enhancers	Stomach Smooth Muscle	stomach
50	chr5:146787200-146796400	Weak transcription	Brain Substantia Nigra	brain

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