Variant report

Variant	rs735822
Chromosome Location	chr13:76209961-76209962
allele	A/C
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	chr13:76209721-76210227	HepG2	liver:	n/a	chr13:76210041-76210057
2	EGR1	chr13:76209721-76210361	ECC-1	luminal epithelium:	n/a	chr13:76210011-76210021 chr13:76210025-76210039 chr13:76210338-76210348 chr13:76209941-76209951 chr13:76210051-76210065
3	ZEB1	chr13:76209834-76210091	GM12878	blood:	n/a	chr13:76209958-76209967 chr13:76209960-76209967 chr13:76210021-76210033 chr13:76210024-76210031
4	MAX	chr13:76209447-76210294	H1-hESC	embryonic stem cell:	n/a	chr13:76209876-76209885 chr13:76209875-76209886
5	PAX5	chr13:76209761-76210337	GM12892	blood:	n/a	n/a
6	MAX	chr13:76209429-76210263	H1-hESC	embryonic stem cell:	n/a	chr13:76209876-76209885 chr13:76209875-76209886
7	TCF7L2	chr13:76209581-76211091	HCT-116	colon:	n/a	chr13:76210635-76210644
8	USF1	chr13:76209756-76209979	HepG2	liver:	n/a	chr13:76209876-76209885 chr13:76209876-76209885
9	POLR2A	chr13:76209759-76211292	ECC-1	luminal epithelium:	n/a	n/a
10	RFX5	chr13:76209267-76210104	HepG2	liver:	n/a	n/a
11	TAF1	chr13:76209616-76209968	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr13:76209606-76212673	IMR90	lung:	n/a	chr13:76211344-76211353
13	EGR1	chr13:76209822-76210018	GM12878	blood:	n/a	chr13:76209941-76209951
14	POLR2A	chr13:76209890-76211232	SK-N-SH	brain:	n/a	n/a
15	ELF1	chr13:76209883-76210943	GM12878	blood:	n/a	chr13:76210229-76210241
16	POLR2A	chr13:76209713-76211295	GM18505	blood:	n/a	n/a
17	EP300	chr13:76209765-76210252	H1-hESC	embryonic stem cell:	n/a	chr13:76210041-76210057
18	EP300	chr13:76209763-76211424	SK-N-SH	brain:	n/a	chr13:76210328-76210344 chr13:76210480-76210496 chr13:76210487-76210503 chr13:76210041-76210057
19	BHLHE40	chr13:76209286-76211225	HepG2	liver:	n/a	chr13:76210232-76210248 chr13:76209876-76209885 chr13:76209876-76209885
20	USF1	chr13:76209731-76210054	H1-hESC	embryonic stem cell:	n/a	chr13:76209876-76209885 chr13:76209876-76209885
21	USF1	chr13:76209742-76210078	H1-hESC	embryonic stem cell:	n/a	chr13:76209876-76209885 chr13:76209876-76209885
22	CTCF	chr13:76209880-76210030	GM12869	blood:	n/a	n/a
23	NFIC	chr13:76209582-76210421	ECC-1	luminal epithelium:	n/a	n/a
24	CEBPB	chr13:76209805-76210195	ECC-1	luminal epithelium:	n/a	n/a
25	TCF7L2	chr13:76209874-76211070	Hela-S3	cervix:	n/a	chr13:76210635-76210644
26	FOXM1	chr13:76209725-76211097	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr13:76209737-76211304	GM12892	blood:	n/a	n/a
28	YY1	chr13:76209891-76210329	GM12892	blood:	n/a	chr13:76210032-76210041
29	TCF12	chr13:76209762-76210174	H1-hESC	embryonic stem cell:	n/a	chr13:76210009-76210016
30	MAX	chr13:76209416-76211328	ECC-1	luminal epithelium:	n/a	chr13:76209876-76209885 chr13:76209875-76209886 chr13:76211308-76211318
31	EGR1	chr13:76209809-76210274	GM12878	blood:	n/a	chr13:76210011-76210021 chr13:76210025-76210039 chr13:76209941-76209951 chr13:76210051-76210065
32	MYC	chr13:76209754-76210051	MCF-7	breast:	n/a	chr13:76209876-76209885 chr13:76209875-76209886
33	POLR2A	chr13:76209539-76211273	H1-hESC	embryonic stem cell:	n/a	n/a
34	HA-E2F1	chr13:76209789-76210892	Hela-S3	cervix:	n/a	chr13:76209983-76209995 chr13:76209839-76209848 chr13:76210032-76210041
35	ZBTB7A	chr13:76209569-76210416	ECC-1	luminal epithelium:	n/a	n/a
36	TCF7L2	chr13:76209808-76210922	HEK293	kidney:	n/a	chr13:76210635-76210644
37	POLR2A	chr13:76209569-76211298	ECC-1	luminal epithelium:	n/a	n/a
38	BHLHE40	chr13:76209695-76210786	GM12878	blood:	n/a	chr13:76210232-76210248 chr13:76209876-76209885 chr13:76209876-76209885
39	BHLHE40	chr13:76209746-76210008	K562	blood:	n/a	chr13:76209876-76209885 chr13:76209876-76209885
40	RUNX3	chr13:76209471-76211208	GM12878	blood:	n/a	n/a
41	ESR1	chr13:76209778-76210160	ECC-1	luminal epithelium:	n/a	n/a
42	NFIC	chr13:76209632-76210767	ECC-1	luminal epithelium:	n/a	n/a
43	SP1	chr13:76209868-76210361	H1-hESC	embryonic stem cell:	n/a	chr13:76210226-76210235 chr13:76210224-76210236 chr13:76210224-76210236
44	SMARCB1	chr13:76209824-76211304	Hela-S3	cervix:	n/a	n/a
45	MAZ	chr13:76209615-76210892	Hela-S3	cervix:	n/a	chr13:76209876-76209885 chr13:76209875-76209886
46	EP300	chr13:76209594-76210413	ECC-1	luminal epithelium:	n/a	chr13:76210328-76210344 chr13:76210041-76210057
47	MAX	chr13:76209871-76210206	GM12878	blood:	n/a	chr13:76209876-76209885 chr13:76209875-76209886
48	PBX3	chr13:76209846-76210775	SK-N-SH	brain:	n/a	n/a
49	TEAD4	chr13:76209867-76210220	HepG2	liver:	n/a	n/a
50	E2F6	chr13:76209388-76211970	H1-hESC	embryonic stem cell:	n/a	chr13:76211315-76211324 chr13:76209728-76209740 chr13:76209983-76209995 chr13:76209839-76209848 chr13:76210032-76210041 chr13:76209560-76209572 chr13:76209568-76209577 chr13:76211075-76211084 chr13:76209408-76209415

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76194856..76197534-chr13:76208958..76210482,2	MCF-7	breast:

Variant related genes	Relation type
LMO7	TF binding region
ENSG00000136153	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1006408	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10507832	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11616974	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1323692	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1570542	0.91[ASN][1000 genomes]
rs1951832	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885336	0.84[ASN][1000 genomes]
rs55825533	0.88[ASN][1000 genomes]
rs68028935	0.85[ASN][1000 genomes]
rs7995740	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7996197	0.92[ASN][1000 genomes]
rs9285297	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9318364	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9593109	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9600511	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751152	chr13:76144199-76288418	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv976062	chr13:76206320-76211659	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1816393	chr13:76207565-76210742	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3425803	chr13:76208851-76211849	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv13276	chr13:76209699-76211118	Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1818390	chr13:76209750-76211044	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv562348	chr13:76209779-76210579	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv562349	chr13:76209779-76210639	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1791932	chr13:76209779-76210854	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1796506	chr13:76209779-76210854	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1837143	chr13:76209779-76210854	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1843026	chr13:76209779-76210854	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv562350	chr13:76209779-76210854	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv562351	chr13:76209779-76210992	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv1797534	chr13:76209779-76211057	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1800577	chr13:76209779-76211057	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv1803232	chr13:76209779-76211057	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv1836179	chr13:76209779-76211623	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv1838622	chr13:76209779-76211623	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv562352	chr13:76209881-76210639	Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv562353	chr13:76209881-76210890	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv562354	chr13:76209881-76210992	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv562355	chr13:76209881-76211057	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs735822	RP11-173B14.5	cis	Adipose Subcutaneous	GTEx
rs735822	RP11-173B14.5	cis	Artery Tibial	GTEx
rs735822	RP11-173B14.5	cis	Skin Sun Exposed Lower leg	GTEx
rs735822	RP11-173B14.5	cis	Artery Aorta	GTEx
rs735822	RP11-173B14.5	cis	Nerve Tibial	GTEx
rs735822	RP11-173B14.5	cis	lung	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76208000-76211600	Active TSS	Osteobl	bone
2	chr13:76208600-76210600	Active TSS	Placenta	Placenta
3	chr13:76208600-76211400	Active TSS	Muscle Satellite Cultured Cells	--
4	chr13:76208600-76211800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr13:76208600-76215000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:76209000-76212000	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr13:76209000-76212200	Active TSS	HSMM	muscle
8	chr13:76209000-76214400	Active TSS	NHDF-Ad	bronchial
9	chr13:76209200-76210000	Flanking Active TSS	HepG2	liver
10	chr13:76209200-76210600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr13:76209200-76211400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr13:76209200-76211600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr13:76209200-76211800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr13:76209200-76212000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:76209200-76212200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr13:76209200-76212200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr13:76209200-76213600	Active TSS	NHLF	lung
18	chr13:76209200-76214800	Active TSS	HSMMtube	muscle
19	chr13:76209400-76210000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:76209400-76210200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:76209400-76210600	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr13:76209400-76210600	Active TSS	NHEK	skin
23	chr13:76209400-76210800	Active TSS	Primary T cells from cord blood	blood
24	chr13:76209400-76210800	Active TSS	Fetal Kidney	kidney
25	chr13:76209400-76210800	Active TSS	Pancreas	Pancrea
26	chr13:76209400-76211000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr13:76209400-76211400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr13:76209400-76211400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr13:76209400-76211600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr13:76209400-76211600	Active TSS	Ovary	ovary
31	chr13:76209400-76211800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr13:76209400-76211800	Active TSS	Fetal Lung	lung
33	chr13:76209400-76212000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:76209400-76212200	Active TSS	Aorta	Aorta
35	chr13:76209600-76210000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:76209600-76210000	Enhancers	Primary B cells from peripheral blood	blood
37	chr13:76209600-76210000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr13:76209600-76210000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr13:76209600-76210000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:76209600-76210000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr13:76209600-76210000	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr13:76209600-76210000	Active TSS	Liver	Liver
43	chr13:76209600-76210000	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr13:76209600-76210000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
45	chr13:76209600-76210000	Flanking Active TSS	Esophagus	oesophagus
46	chr13:76209600-76210000	Flanking Active TSS	Gastric	stomach
47	chr13:76209600-76210000	Flanking Active TSS	Right Atrium	heart
48	chr13:76209600-76210000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr13:76209600-76210000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr13:76209600-76210000	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links