Variant report

Variant	rs2713736
Chromosome Location	chr3:158520483-158520484
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	CTCF	chr3:158520340-158520490	RPTEC	kidney:	n/a	n/a
2	RCOR1	chr3:158519379-158520799	K562	blood:	n/a	n/a
3	TBL1XR1	chr3:158520273-158520563	K562	blood:	n/a	n/a
4	MAX	chr3:158518993-158520599	HepG2	liver:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
5	POLR2A	chr3:158519310-158521018	HL-60	blood:	n/a	n/a
6	MAX	chr3:158519606-158520520	Hela-S3	cervix:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
7	POLR2A	chr3:158518843-158520542	IMR90	lung:	n/a	n/a
8	NR2F2	chr3:158519337-158520658	K562	blood:	n/a	n/a
9	CTCF	chr3:158520360-158520510	K562	blood:	n/a	n/a
10	SMARCC1	chr3:158519457-158520646	Hela-S3	cervix:	n/a	n/a
11	RCOR1	chr3:158520238-158520640	K562	blood:	n/a	n/a
12	POLR2A	chr3:158519428-158520581	NB4	blood:	n/a	n/a
13	MYC	chr3:158520297-158520511	H1-hESC	embryonic stem cell:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520435-158520450
14	CTCF	chr3:158520420-158520570	GM12868	blood:	n/a	n/a
15	USF1	chr3:158519436-158520650	K562	blood:	n/a	n/a
16	CTCF	chr3:158520200-158520490	AG09319	gingival:	n/a	n/a
17	MYC	chr3:158519286-158520734	K562	blood:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
18	MYC	chr3:158519352-158520748	K562	blood:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
19	MAX	chr3:158519425-158520721	GM12878	blood:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
20	HA-E2F1	chr3:158518788-158520590	MCF-7	breast:	n/a	n/a
21	MAX	chr3:158519262-158520556	A549	lung:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
22	SMARCB1	chr3:158519420-158520659	Hela-S3	cervix:	n/a	n/a
23	SIN3A	chr3:158519005-158520527	H1-hESC	embryonic stem cell:	n/a	chr3:158519699-158519713
24	USF2	chr3:158520337-158520555	K562	blood:	n/a	n/a
25	USF2	chr3:158519354-158520622	GM12878	blood:	n/a	chr3:158519843-158519854 chr3:158519825-158519836
26	BHLHE40	chr3:158519156-158520576	HepG2	liver:	n/a	n/a
27	CTCF	chr3:158520420-158520570	SK-N-SH_RA	brain:	n/a	n/a
28	REST	chr3:158519326-158520647	HL-60	blood:	n/a	chr3:158519590-158519603 chr3:158519585-158519603
29	POLR2A	chr3:158518781-158520577	K562	blood:	n/a	n/a
30	HCFC1	chr3:158518599-158520668	Hela-S3	cervix:	n/a	n/a
31	MAX	chr3:158519162-158521191	NB4	blood:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
32	MAX	chr3:158519466-158520488	H1-hESC	embryonic stem cell:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
33	POLR2A	chr3:158519030-158520515	GM12878	blood:	n/a	n/a
34	CBX3	chr3:158520121-158520763	K562	blood:	n/a	n/a
35	USF1	chr3:158519517-158520512	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:158519298-158520569	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:158519072-158520567	HepG2	liver:	n/a	n/a
38	MYC	chr3:158519420-158520741	K562	blood:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
39	E2F6	chr3:158519424-158520504	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:158519546-158520502	Hela-S3	cervix:	n/a	n/a
41	SPI1	chr3:158520175-158520642	HL-60	blood:	n/a	chr3:158520422-158520435
42	GTF2F1	chr3:158520308-158520564	K562	blood:	n/a	n/a
43	USF1	chr3:158519422-158520499	A549	lung:	n/a	n/a
44	CHD2	chr3:158519373-158520506	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:158519348-158520513	K562	blood:	n/a	n/a
46	MXI1	chr3:158520320-158520510	K562	blood:	n/a	chr3:158520438-158520447
47	POLR2A	chr3:158519093-158520514	GM19099	blood:	n/a	n/a
48	MAX	chr3:158519367-158520684	H1-hESC	embryonic stem cell:	n/a	chr3:158520438-158520447 chr3:158520436-158520446 chr3:158520189-158520198 chr3:158520435-158520450
49	CEBPB	chr3:158520443-158521023	K562	blood:	n/a	chr3:158520837-158520848
50	MXI1	chr3:158518622-158520812	IMR90	lung:	n/a	chr3:158520438-158520447

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158519080..158523533-chr3:158523571..158529220,8	MCF-7	breast:
2	chr3:158519555..158521596-chr3:158521665..158523312,3	MCF-7	breast:

Variant related genes	Relation type
MFSD1	TF binding region
ENSG00000272247	TF binding region
ENSG00000118855	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10936160	0.88[ASN][1000 genomes]
rs12493280	0.88[ASN][1000 genomes]
rs12638831	0.88[ASN][1000 genomes]
rs1381463	0.88[ASN][1000 genomes]
rs2244996	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364921	0.95[ASN][1000 genomes]
rs2615052	0.82[EUR][1000 genomes]
rs6802844	0.97[ASN][1000 genomes]
rs7429205	0.89[ASN][1000 genomes]
rs9861042	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2713736	RP11-379F4.9	cis	Thyroid	GTEx
rs2713736	RP11-379F4.9	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158518600-158520600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:158518600-158521400	Active TSS	Brain Cingulate Gyrus	brain
3	chr3:158518800-158520600	Active TSS	Fetal Heart	heart
4	chr3:158518800-158520600	Active TSS	Left Ventricle	heart
5	chr3:158518800-158520600	Active TSS	Pancreas	Pancrea
6	chr3:158518800-158520800	Active TSS	Colonic Mucosa	Colon
7	chr3:158518800-158520800	Active TSS	Fetal Intestine Large	intestine
8	chr3:158518800-158520800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:158518800-158521200	Active TSS	Psoas Muscle	Psoas
10	chr3:158518800-158521400	Active TSS	Brain Hippocampus Middle	brain
11	chr3:158518800-158522000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:158519000-158520600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:158519000-158520600	Active TSS	Esophagus	oesophagus
14	chr3:158519000-158520800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:158519000-158520800	Active TSS	Aorta	Aorta
16	chr3:158519000-158520800	Active TSS	Brain Angular Gyrus	brain
17	chr3:158519000-158520800	Active TSS	Ovary	ovary
18	chr3:158519000-158520800	Active TSS	A549	lung
19	chr3:158519000-158521000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:158519000-158521000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr3:158519000-158521200	Active TSS	Brain Substantia Nigra	brain
22	chr3:158519000-158521400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:158519200-158520600	Active TSS	Colon Smooth Muscle	Colon
24	chr3:158519200-158520800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:158519200-158520800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:158519200-158520800	Active TSS	Fetal Stomach	stomach
27	chr3:158519200-158521000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:158519200-158521000	Active TSS	Right Ventricle	heart
29	chr3:158519200-158521400	Active TSS	Rectal Smooth Muscle	rectum
30	chr3:158519200-158521600	Active TSS	Right Atrium	heart
31	chr3:158519400-158520600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:158519400-158520600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr3:158519400-158520600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:158519400-158520600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:158519400-158520600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:158519400-158520600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:158519400-158520600	Active TSS	Duodenum Mucosa	Duodenum
38	chr3:158519400-158520600	Active TSS	Fetal Kidney	kidney
39	chr3:158519400-158520600	Active TSS	Gastric	stomach
40	chr3:158519400-158520600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr3:158519400-158520600	Active TSS	Small Intestine	intestine
42	chr3:158519400-158520600	Active TSS	Spleen	Spleen
43	chr3:158519400-158521000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr3:158519400-158521000	Active TSS	Fetal Intestine Small	intestine
45	chr3:158519400-158521000	Active TSS	NHLF	lung
46	chr3:158519400-158521200	Active TSS	K562	blood
47	chr3:158519600-158520600	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:158519600-158520600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:158519600-158520600	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr3:158519600-158520600	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links