Variant report

Variant	rs3794540
Chromosome Location	chr15:52427081-52427082
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	RAD21	chr15:52426697-52427137	HepG2	liver:	n/a	n/a
2	MBD4	chr15:52426584-52427227	HepG2	liver:	n/a	n/a
3	USF2	chr15:52426751-52427136	HepG2	liver:	n/a	n/a
4	MYBL2	chr15:52426368-52427243	HepG2	liver:	n/a	n/a
5	RXRA	chr15:52426716-52427153	HepG2	liver:	n/a	chr15:52426904-52426918 chr15:52426976-52426996
6	CREB1	chr15:52426636-52427227	HepG2	liver:	n/a	n/a
7	RAD21	chr15:52426627-52427231	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:52426522-52427266	HepG2	liver:	n/a	n/a
9	SMC3	chr15:52426728-52427156	HepG2	liver:	n/a	n/a
10	MAX	chr15:52426822-52427175	HepG2	liver:	n/a	n/a
11	EP300	chr15:52426648-52427098	HepG2	liver:	n/a	n/a
12	HNF4A	chr15:52426739-52427152	HepG2	liver:	n/a	chr15:52426906-52426918 chr15:52426904-52426919 chr15:52426903-52426921
13	MXI1	chr15:52426665-52427218	HepG2	liver:	n/a	n/a
14	RCOR1	chr15:52426543-52427360	HepG2	liver:	n/a	n/a
15	NFIC	chr15:52426667-52427144	HepG2	liver:	n/a	n/a
16	EP300	chr15:52426667-52427238	HepG2	liver:	n/a	n/a
17	CHD2	chr15:52426706-52427192	HepG2	liver:	n/a	n/a
18	USF1	chr15:52426792-52427099	HepG2	liver:	n/a	chr15:52426939-52426950
19	HNF4G	chr15:52426575-52427248	HepG2	liver:	n/a	chr15:52426906-52426918 chr15:52426903-52426918 chr15:52426903-52426921
20	JUND	chr15:52426694-52427143	HepG2	liver:	n/a	n/a
21	HEY1	chr15:52426589-52427099	HepG2	liver:	n/a	n/a
22	EP300	chr15:52426725-52427123	HepG2	liver:	n/a	n/a
23	POLR2A	chr15:52426756-52427089	HepG2	liver:	n/a	n/a
24	POLR2A	chr15:52426677-52427368	HepG2	liver:	n/a	n/a
25	RFX5	chr15:52426807-52427131	HepG2	liver:	n/a	n/a
26	USF1	chr15:52426806-52427104	K562	blood:	n/a	chr15:52426939-52426950
27	SREBP1	chr15:52426752-52427144	HepG2	liver:	n/a	chr15:52426941-52426950 chr15:52426941-52426950
28	MYBL2	chr15:52426564-52427194	HepG2	liver:	n/a	n/a
29	FOXA1	chr15:52426683-52427375	HepG2	liver:	n/a	n/a
30	SREBP1	chr15:52426796-52427141	HepG2	liver:	n/a	chr15:52426941-52426950 chr15:52426941-52426950
31	HNF4A	chr15:52426654-52427185	HepG2	liver:	n/a	chr15:52426906-52426918 chr15:52426904-52426919 chr15:52426903-52426921
32	HNF4G	chr15:52426689-52427137	HepG2	liver:	n/a	chr15:52426906-52426918 chr15:52426903-52426918 chr15:52426903-52426921
33	ARID3A	chr15:52426739-52427118	HepG2	liver:	n/a	n/a
34	HDAC2	chr15:52426673-52427090	HepG2	liver:	n/a	n/a
35	MAX	chr15:52427048-52428973	NB4	blood:	n/a	chr15:52427919-52427929
36	POLR2A	chr15:52426683-52427120	HepG2	liver:	n/a	n/a
37	NFIC	chr15:52426619-52427090	HepG2	liver:	n/a	n/a
38	JUND	chr15:52426737-52427133	HepG2	liver:	n/a	n/a
39	POLR2A	chr15:52426650-52427093	HepG2	liver:	n/a	n/a
40	FOXA2	chr15:52426716-52427244	HepG2	liver:	n/a	n/a
41	USF1	chr15:52426734-52427138	HepG2	liver:	n/a	chr15:52426939-52426950
42	HNF4A	chr15:52426736-52427291	HepG2	liver:	n/a	chr15:52426906-52426918 chr15:52426904-52426919 chr15:52426903-52426921
43	BHLHE40	chr15:52426712-52427351	HepG2	liver:	n/a	n/a
44	SPI1	chr15:52426866-52427414	HL-60	blood:	n/a	chr15:52427128-52427141
45	CREB1	chr15:52426635-52427362	HepG2	liver:	n/a	n/a
46	RAD21	chr15:52426743-52427163	HepG2	liver:	n/a	n/a
47	FOSL2	chr15:52426678-52427235	HepG2	liver:	n/a	n/a
48	POLR2A	chr15:52426766-52427104	HepG2	liver:	n/a	n/a
49	SP1	chr15:52426609-52427266	HepG2	liver:	n/a	chr15:52427123-52427136

No.	Distal block	Cell Line	Cell type
1	chr15:52419606..52421639-chr15:52426759..52428564,2	K562	blood:
2	chr15:52309643..52312109-chr15:52424380..52429568,4	MCF-7	breast:
3	chr15:52420540..52423149-chr15:52426154..52427848,2	MCF-7	breast:
4	chr15:52415685..52419897-chr15:52423776..52427123,4	K562	blood:

Variant related genes	Relation type
ENSG00000259709	TF binding region
ENSG00000069966	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000259709	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11070882	0.80[ASN][1000 genomes]
rs11856177	0.80[ASN][1000 genomes]
rs12438169	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12438190	0.86[EUR][1000 genomes]
rs12438194	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12438743	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12438937	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12440956	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12593041	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12595160	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12899030	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12899343	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12901354	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12901730	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12901891	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12902073	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12902522	1.00[CEU][hapmap]
rs12903769	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12904831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907835	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908742	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12908833	0.80[ASN][1000 genomes]
rs12909161	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12909184	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs12909880	0.80[AMR][1000 genomes]
rs12910398	1.00[YRI][hapmap]
rs12912428	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12916557	0.80[ASN][1000 genomes]
rs2227308	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2398	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35709612	0.84[EUR][1000 genomes]
rs35827106	0.80[ASN][1000 genomes]
rs3794543	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4636859	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4638520	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4774608	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4776003	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4776007	0.91[CEU][hapmap]
rs62014721	0.85[EUR][1000 genomes]
rs62014722	0.84[EUR][1000 genomes]
rs7164508	1.00[YRI][hapmap]
rs8034097	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3794540	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52404800-52428000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:52405000-52427400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:52405000-52427800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:52405000-52428800	Weak transcription	Fetal Heart	heart
5	chr15:52406400-52427800	Weak transcription	Fetal Brain Male	brain
6	chr15:52407400-52427600	Weak transcription	HSMMtube	muscle
7	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
8	chr15:52407800-52428800	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
10	chr15:52408800-52428000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:52410000-52428600	Weak transcription	Hela-S3	cervix
12	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:52410600-52427800	Weak transcription	Adipose Nuclei	Adipose
14	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:52411200-52428600	Weak transcription	Left Ventricle	heart
16	chr15:52412000-52427200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:52412000-52427800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:52412200-52436000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:52413600-52431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:52413800-52428400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:52414200-52427800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr15:52414400-52428400	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:52416000-52427800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:52416000-52432800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:52416200-52431600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:52417000-52427600	Weak transcription	HSMM	muscle
28	chr15:52417000-52436000	Weak transcription	Lung	lung
29	chr15:52417200-52428600	Weak transcription	NHLF	lung
30	chr15:52417200-52428800	Weak transcription	Gastric	stomach
31	chr15:52417200-52431200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:52417200-52431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:52417200-52436200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr15:52417400-52429000	Weak transcription	K562	blood
35	chr15:52417400-52431800	Weak transcription	HMEC	breast
36	chr15:52417400-52432000	Weak transcription	NHDF-Ad	bronchial
37	chr15:52417600-52435400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:52417800-52431800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:52418000-52427400	Weak transcription	GM12878-XiMat	blood
40	chr15:52418200-52428000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:52418800-52427600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:52420000-52427400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:52420200-52427800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:52420400-52433600	Strong transcription	Ovary	ovary
45	chr15:52420800-52427400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr15:52421800-52431800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:52422000-52427600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:52422200-52427800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr15:52422200-52428200	Strong transcription	Primary T cells from cord blood	blood
50	chr15:52422200-52428400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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