Variant report

Variant	rs11130345
Chromosome Location	chr3:53189670-53189671
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	EP300	chr3:53189581-53190224	ECC-1	luminal epithelium:	n/a	n/a
2	ZNF263	chr3:53189531-53189928	HEK293-T-REx	kidney:	n/a	n/a
3	HDAC2	chr3:53189628-53190172	MCF-7	breast:	n/a	n/a
4	FOXM1	chr3:53189649-53190234	MCF-7	breast:	n/a	n/a
5	HDAC2	chr3:53189602-53190321	MCF-7	breast:	n/a	chr3:53190262-53190276 chr3:53190263-53190277 chr3:53190257-53190271 chr3:53190258-53190272 chr3:53190260-53190274 chr3:53190261-53190275
6	TCF12	chr3:53189418-53190614	MCF-7	breast:	n/a	n/a
7	MAX	chr3:53189548-53190679	MCF-7	breast:	n/a	chr3:53189786-53189796
8	EP300	chr3:53189589-53190231	MCF-7	breast:	n/a	n/a
9	TCF12	chr3:53189596-53190309	ECC-1	luminal epithelium:	n/a	n/a
10	SIN3AK20	chr3:53189493-53190714	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:53189660-53189996	ECC-1	luminal epithelium:	n/a	n/a
12	EP300	chr3:53189632-53190218	MCF-7	breast:	n/a	n/a
13	MAX	chr3:53189550-53190293	ECC-1	luminal epithelium:	n/a	chr3:53189786-53189796
14	ELF1	chr3:53189617-53190271	MCF-7	breast:	n/a	n/a
15	NR2F2	chr3:53189556-53190266	MCF-7	breast:	n/a	n/a
16	GATA3	chr3:53189471-53190361	MCF-7	breast:	n/a	n/a
17	TCF12	chr3:53189478-53190275	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr3:53189485-53190210	ECC-1	luminal epithelium:	n/a	chr3:53189786-53189796
19	GATA3	chr3:53189633-53190405	MCF-7	breast:	n/a	n/a
20	ZBTB7A	chr3:53189513-53190845	ECC-1	luminal epithelium:	n/a	chr3:53189595-53189609
21	SIN3AK20	chr3:53189615-53190270	MCF-7	breast:	n/a	n/a
22	NFIC	chr3:53189534-53190270	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr3:53189136-53190844	MCF-7	breast:	n/a	n/a
24	NFIC	chr3:53189518-53190654	ECC-1	luminal epithelium:	n/a	n/a
25	NR2F2	chr3:53189525-53190745	MCF-7	breast:	n/a	n/a
26	MAX	chr3:53189615-53190278	MCF-7	breast:	n/a	chr3:53189786-53189796

No.	Distal block	Cell Line	Cell type
1	chr3:53189219..53190940-chr3:53274136..53276946,2	MCF-7	breast:
2	chr3:53163608..53165597-chr3:53189002..53191742,3	K562	blood:
3	chr3:53188104..53190681-chr3:53198828..53201211,3	K562	blood:
4	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
5	chr3:53187844..53191099-chr3:53288490..53291420,3	MCF-7	breast:

Variant related genes	Relation type
PRKCD	TF binding region
ENSG00000163931	Chromatin interaction
ENSG00000163933	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11130344	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130350	0.84[CHD][hapmap]
rs13085294	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2358617	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773729	0.84[CHD][hapmap]
rs4687706	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6778939	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6778964	0.87[CHD][hapmap]
rs6807359	0.87[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7616077	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11130345	SLC38A3	cis	cerebellum	SCAN
rs11130345	GLT8D1	cis	cerebellum	SCAN
rs11130345	MUSTN1	cis	parietal	SCAN
rs11130345	MANF	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53177800-53190200	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr3:53178600-53190200	Enhancers	Colonic Mucosa	Colon
3	chr3:53179000-53190000	Enhancers	Duodenum Mucosa	Duodenum
4	chr3:53182400-53193400	Weak transcription	Psoas Muscle	Psoas
5	chr3:53182400-53193800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:53183200-53194600	Enhancers	Gastric	stomach
7	chr3:53183400-53194600	Enhancers	Pancreas	Pancrea
8	chr3:53183600-53190600	Enhancers	Liver	Liver
9	chr3:53184200-53194400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:53184400-53193800	Enhancers	Adipose Nuclei	Adipose
11	chr3:53184600-53190000	Weak transcription	Spleen	Spleen
12	chr3:53186800-53190200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:53187600-53189800	Enhancers	Lung	lung
14	chr3:53187600-53190400	Enhancers	Brain Anterior Caudate	brain
15	chr3:53187800-53190200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr3:53187800-53190400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:53187800-53190800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:53187800-53191800	Enhancers	HMEC	breast
19	chr3:53187800-53194600	Enhancers	Esophagus	oesophagus
20	chr3:53188000-53192000	Enhancers	Right Atrium	heart
21	chr3:53188000-53192800	Weak transcription	Small Intestine	intestine
22	chr3:53188400-53190200	Enhancers	Left Ventricle	heart
23	chr3:53188600-53191000	Enhancers	Right Ventricle	heart
24	chr3:53188800-53189800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:53188800-53190800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:53188800-53192800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr3:53189000-53189800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:53189000-53190200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:53189000-53190200	Bivalent Enhancer	Fetal Intestine Small	intestine
30	chr3:53189200-53189800	Enhancers	Hela-S3	cervix
31	chr3:53189200-53191200	Bivalent Enhancer	Placenta	Placenta
32	chr3:53189200-53191800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
33	chr3:53189400-53190200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:53189400-53190600	Bivalent Enhancer	NHEK	skin
35	chr3:53189600-53189800	Enhancers	Aorta	Aorta
36	chr3:53189600-53189800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:53189600-53190200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:53189600-53190200	Bivalent Enhancer	Fetal Lung	lung
39	chr3:53189600-53190400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:53189600-53190400	Bivalent Enhancer	HepG2	liver
41	chr3:53189600-53190600	Enhancers	Brain Substantia Nigra	brain
42	chr3:53189600-53190600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr3:53189600-53191400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
44	chr3:53189600-53191400	Bivalent Enhancer	Fetal Intestine Large	intestine
45	chr3:53189600-53194000	Enhancers	Stomach Mucosa	stomach

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