Variant report

Variant	rs4776003
Chromosome Location	chr15:52404934-52404935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr15:52404377-52404974	GM12892	blood:	n/a	n/a
2	E2F6	chr15:52404006-52405001	H1-hESC	embryonic stem cell:	n/a	chr15:52404011-52404018 chr15:52404974-52404983
3	POLR2A	chr15:52403762-52405802	NB4	blood:	n/a	n/a
4	POLR2A	chr15:52403715-52405006	GM19193	blood:	n/a	n/a
5	POLR2A	chr15:52404322-52404985	GM18951	blood:	n/a	n/a
6	YY1	chr15:52403922-52405027	GM12878	blood:	n/a	chr15:52404972-52404986 chr15:52404061-52404071
7	POLR2A	chr15:52403564-52404976	GM12891	blood:	n/a	n/a
8	YY1	chr15:52404448-52404972	GM12891	blood:	n/a	n/a
9	STAT5A	chr15:52404442-52404992	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:52404206-52404973	GM12878	blood:	n/a	n/a
11	MAX	chr15:52404933-52405322	NB4	blood:	n/a	chr15:52405114-52405130 chr15:52405125-52405132 chr15:52405121-52405136
12	POLR2A	chr15:52404092-52404988	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:52404242-52404968	GM12878	blood:	n/a	n/a
14	MAX	chr15:52404172-52404998	MCF-7	breast:	n/a	n/a
15	CTCF	chr15:52404800-52404950	GM12871	blood:	n/a	chr15:52404927-52404940
16	MYC	chr15:52404760-52405675	NB4	blood:	n/a	chr15:52405114-52405130 chr15:52405125-52405132 chr15:52405121-52405136
17	YY1	chr15:52403896-52404994	GM12878	blood:	n/a	chr15:52404972-52404986 chr15:52404061-52404071
18	POLR2A	chr15:52404328-52404956	GM12892	blood:	n/a	n/a
19	PAX5	chr15:52404718-52404992	GM12892	blood:	n/a	n/a
20	POLR2A	chr15:52403797-52404959	GM12891	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:52404887-52404937	Hela-S3	cervix:	n/a
2	chr15:52404887-52404937	Caco-2	colon:	n/a
3	chr15:52404887-52404937	NT2-D1	testis:	n/a
4	chr15:52404887-52404937	AG04450	lung:	fetal
5	chr15:52404887-52404937	NHDF-neo	bronchial:	n/a
6	chr15:52404887-52404937	LNCaP	prostate:	n/a
7	chr15:52404887-52404937	NH-A	brain:	n/a
8	chr15:52404887-52404937	MCF-7	breast:	n/a
9	chr15:52404887-52404937	BE2_C	brain:	n/a
10	chr15:52404887-52404937	HEEpiC	esophagus:	n/a
11	chr15:52404887-52404937	HUVEC	blood vessel:	n/a
12	chr15:52404887-52404937	HRCEpiC	kidney:	n/a
13	chr15:52404887-52404937	HMEC	breast:	n/a
14	chr15:52404887-52404937	K562	blood:	n/a
15	chr15:52404887-52404937	HRE	kidney:	n/a
16	chr15:52404887-52404937	NB4	blood:	n/a
17	chr15:52404887-52404937	U87	brain:	n/a
18	chr15:52404887-52404937	SK-N-MC	brain:	n/a
19	chr15:52404887-52404937	SK-N-SH_RA	brain:	n/a
20	chr15:52404887-52404937	ECC-1	luminal epithelium:	n/a
21	chr15:52404887-52404937	H1-hESC	embryonic stem cell:	embryo
22	chr15:52404887-52404937	NHBE	bronchial:	n/a
23	chr15:52404887-52404937	Jurkat	blood:	n/a
24	chr15:52404887-52404937	AoSMC	blood vessel:	n/a
25	chr15:52404887-52404937	HCPEpiC	choroid plexus:	n/a
26	chr15:52404887-52404937	GM12892	blood:	n/a
27	chr15:52404887-52404937	HAEpiC	amniotic membrane:	n/a
28	chr15:52404887-52404937	HCF	heart:	n/a
29	chr15:52404887-52404937	ovcar-3	ovarian:	n/a
30	chr15:52404887-52404937	SK-N-SH	brain:	n/a
31	chr15:52404887-52404937	HPAEpiC	pulmonary alveolar:	n/a
32	chr15:52404887-52404937	PFSK-1	brain:	n/a
33	chr15:52404887-52404937	CMK	blood:	n/a
34	chr15:52404887-52404937	HepG2	liver:	n/a
35	chr15:52404887-52404937	HCM	heart:	n/a
36	chr15:52404887-52404937	AG09319	gingival:	n/a
37	chr15:52404887-52404937	HNPCEpiC	eye:	n/a
38	chr15:52404887-52404937	PANC-1	pancreas:	n/a
39	chr15:52404887-52404937	AG10803	skin:	n/a
40	chr15:52404887-52404937	ProgFib	skin:	n/a
41	chr15:52404887-52404937	SAEC	small airway:	n/a
42	chr15:52404887-52404937	HCT-116	colon:	n/a
43	chr15:52404887-52404937	HRPEpiC	eye:	n/a
44	chr15:52404887-52404937	HEK293	kidney:	embryo
45	chr15:52404887-52404937	GM12878	blood:	n/a
46	chr15:52404887-52404937	MCF10A-Er-Src	breast:	n/a
47	chr15:52404887-52404937	PrEC	prostate:	n/a
48	chr15:52404887-52404937	GM12891	blood:	n/a
49	chr15:52404887-52404937	T-47D	breast:	n/a
50	chr15:52404887-52404937	A549	lung:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52263208..52265625-chr15:52404085..52407650,4	MCF-7	breast:
2	chr15:52404587..52406331-chr15:52432467..52434245,2	MCF-7	breast:
3	chr15:52403961..52406655-chr15:52470750..52472609,2	MCF-7	breast:
4	chr15:52404464..52407280-chr15:52415315..52418015,2	MCF-7	breast:
5	chr15:52309956..52312123-chr15:52404856..52406463,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259327	TF binding region
ENSG00000259327	CpG island
ENSG00000069966	Chromatin interaction
ENSG00000259709	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11070882	0.82[ASN][1000 genomes]
rs11856177	0.82[ASN][1000 genomes]
rs12438194	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12438743	0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs12438937	0.93[GIH][hapmap]
rs12440956	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593041	0.93[GIH][hapmap]
rs12593936	0.81[MEX][hapmap]
rs12594679	0.81[ASN][1000 genomes]
rs12595160	0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12899030	0.93[GIH][hapmap]
rs12899343	0.93[GIH][hapmap]
rs12901354	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901730	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12901891	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12902073	0.86[ASN][1000 genomes]
rs12903769	0.88[ASN][1000 genomes]
rs12904831	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12904889	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12907835	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12908742	0.86[ASN][1000 genomes]
rs12908833	0.82[ASN][1000 genomes]
rs12909161	0.85[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12909184	0.89[GIH][hapmap]
rs12912428	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916557	0.82[ASN][1000 genomes]
rs2227308	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2231297	1.00[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2398	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414130	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2414132	0.93[CEU][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs34283892	0.81[ASN][1000 genomes]
rs35827106	0.82[ASN][1000 genomes]
rs3794540	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3794543	0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs4238384	0.83[GIH][hapmap]
rs4636859	0.90[ASN][1000 genomes]
rs4638520	0.93[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes]
rs4774608	0.91[ASN][1000 genomes]
rs8034097	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4776003	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:52402400-52405600	Weak transcription	HepG2	liver
3	chr15:52404000-52405000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:52404000-52405000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr15:52404000-52405000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:52404000-52405000	Active TSS	Brain Angular Gyrus	brain
7	chr15:52404000-52405000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
8	chr15:52404000-52405000	Active TSS	Esophagus	oesophagus
9	chr15:52404000-52405000	Bivalent Enhancer	Placenta	Placenta
10	chr15:52404000-52405000	Enhancers	Gastric	stomach
11	chr15:52404000-52405000	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr15:52404000-52405400	Enhancers	Spleen	Spleen
13	chr15:52404200-52405000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr15:52404200-52405000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:52404200-52405000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:52404200-52405000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr15:52404200-52405000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:52404200-52405000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:52404200-52405000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:52404200-52405000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:52404200-52405000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:52404200-52405000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr15:52404200-52405000	Active TSS	Fetal Brain Female	brain
24	chr15:52404200-52405000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
25	chr15:52404200-52405000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
26	chr15:52404200-52405000	Bivalent/Poised TSS	Thymus	Thymus
27	chr15:52404200-52405000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
28	chr15:52404200-52405000	Bivalent/Poised TSS	Osteobl	bone
29	chr15:52404400-52405000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:52404400-52405000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:52404400-52405000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr15:52404400-52405000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr15:52404400-52405000	Active TSS	Primary T cells from cord blood	blood
34	chr15:52404400-52405000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr15:52404400-52405000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:52404400-52405000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:52404400-52405000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr15:52404400-52405000	Active TSS	Brain Substantia Nigra	brain
39	chr15:52404400-52405000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr15:52404400-52405000	Active TSS	Psoas Muscle	Psoas
41	chr15:52404400-52405000	Active TSS	Right Atrium	heart
42	chr15:52404400-52405000	Flanking Active TSS	Right Ventricle	heart
43	chr15:52404400-52405000	Flanking Active TSS	HMEC	breast
44	chr15:52404400-52405200	Active TSS	Primary hematopoietic stem cells	blood
45	chr15:52404600-52405000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:52404600-52405000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:52404600-52405000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr15:52404600-52405000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:52404600-52405000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:52404600-52405000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum

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