Variant report

Variant	rs2071386
Chromosome Location	chr3:139258508-139258509
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	POLR2A	chr3:139258251-139258881	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr3:139254870-139260531	SK-N-SH	brain:	n/a	n/a
3	REST	chr3:139258241-139258808	SK-N-SH	brain:	n/a	chr3:139258260-139258273
4	POLR2A	chr3:139258508-139258890	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:139258148-139258866	ECC-1	luminal epithelium:	n/a	n/a
6	ZBTB7A	chr3:139258134-139258900	ECC-1	luminal epithelium:	n/a	n/a
7	GTF2F1	chr3:139258486-139258793	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr3:139258186-139258780	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:139258094-139258940	H1-neurons	neurons:	n/a	n/a
10	REST	chr3:139257951-139259122	H1-neurons	neurons:	n/a	chr3:139258140-139258153 chr3:139258260-139258273
11	EP300	chr3:139251629-139259175	SK-N-SH	brain:	n/a	chr3:139256357-139256366 chr3:139253631-139253641 chr3:139252024-139252040 chr3:139256356-139256365
12	TCF12	chr3:139258352-139258666	H1-hESC	embryonic stem cell:	n/a	n/a
13	HA-E2F1	chr3:139258043-139258844	MCF-7	breast:	n/a	n/a
14	SIN3AK20	chr3:139256022-139258994	HCT-116	colon:	n/a	n/a
15	POLR2A	chr3:139257979-139259222	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr3:139258245-139258881	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:139258341-139258873	HCT-116	colon:	n/a	n/a
18	MXI1	chr3:139258311-139258820	H1-hESC	embryonic stem cell:	n/a	n/a
19	YY1	chr3:139258343-139258786	SK-N-SH_RA	brain:	n/a	n/a
20	MAX	chr3:139258205-139258949	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr3:139258165-139258820	H1-hESC	embryonic stem cell:	n/a	n/a
22	EP300	chr3:139258367-139258748	SK-N-SH_RA	brain:	n/a	n/a
23	SIN3A	chr3:139257675-139258966	H1-hESC	embryonic stem cell:	n/a	chr3:139258137-139258150
24	FOXP2	chr3:139258249-139258654	SK-N-MC	brain:	n/a	n/a
25	TCF12	chr3:139258083-139258843	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr3:139258185-139259063	H1-hESC	embryonic stem cell:	n/a	n/a
27	CHD2	chr3:139258368-139258630	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:139258220-139258938	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr3:139258058-139258989	H1-neurons	neurons:	n/a	n/a
30	TCF12	chr3:139258303-139258624	H1-hESC	embryonic stem cell:	n/a	n/a
31	TBP	chr3:139258215-139259010	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr3:139258135-139258898	ECC-1	luminal epithelium:	n/a	n/a
33	EBF1	chr3:139258489-139259021	GM12878	blood:	n/a	chr3:139258800-139258811
34	TAF1	chr3:139258203-139259152	H1-hESC	embryonic stem cell:	n/a	n/a
35	TAF1	chr3:139258313-139258874	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr3:139258238-139258979	HCT-116	colon:	n/a	n/a
37	YY1	chr3:139258356-139258743	HCT-116	colon:	n/a	n/a
38	YY1	chr3:139258144-139258850	H1-hESC	embryonic stem cell:	n/a	n/a
39	MYC	chr3:139258466-139258820	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:139258265-139258834	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr3:139258400-139258550	HA-sp	spinal cord:	n/a	n/a
42	YY1	chr3:139258338-139258760	HepG2	liver:	n/a	n/a
43	YY1	chr3:139258280-139258954	SK-N-SH_RA	brain:	n/a	n/a
44	YY1	chr3:139258332-139258835	H1-hESC	embryonic stem cell:	n/a	n/a
45	ZNF143	chr3:139258243-139258805	H1-hESC	embryonic stem cell:	n/a	n/a
46	YY1	chr3:139258237-139258848	ECC-1	luminal epithelium:	n/a	n/a
47	TCF12	chr3:139258117-139258867	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr3:139258318-139258819	SK-N-SH	brain:	n/a	n/a
49	ZBTB7A	chr3:139258060-139258799	ECC-1	luminal epithelium:	n/a	n/a
50	UBTF	chr3:139258359-139258604	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000248932	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11921723	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922772	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492518	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57253122	0.87[AFR][1000 genomes]
rs6786021	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799670	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802598	0.83[AMR][1000 genomes];0.91[EUR][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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139251800-139258600	Enhancers	Fetal Heart	heart
2	chr3:139257400-139259400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:139257600-139258600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
4	chr3:139257600-139259000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:139257600-139259000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr3:139257600-139259200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:139257600-139259200	Active TSS	Fetal Kidney	kidney
8	chr3:139257600-139259200	Active TSS	Fetal Lung	lung
9	chr3:139257600-139259400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:139257600-139259400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:139257600-139259400	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:139257600-139259800	Active TSS	Ovary	ovary
13	chr3:139257800-139258600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr3:139257800-139258600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
15	chr3:139257800-139258600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
16	chr3:139257800-139258600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:139257800-139258600	Flanking Active TSS	Placenta	Placenta
18	chr3:139257800-139258600	Active TSS	HSMM	muscle
19	chr3:139257800-139258800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:139257800-139259000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr3:139257800-139259000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:139257800-139259000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
23	chr3:139257800-139259000	Active TSS	Colon Smooth Muscle	Colon
24	chr3:139257800-139259000	Active TSS	Psoas Muscle	Psoas
25	chr3:139257800-139259000	Active TSS	Right Ventricle	heart
26	chr3:139257800-139259000	Flanking Active TSS	HMEC	breast
27	chr3:139257800-139259000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
28	chr3:139257800-139259200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:139257800-139259200	Active TSS	Aorta	Aorta
30	chr3:139257800-139259200	Active TSS	Fetal Intestine Small	intestine
31	chr3:139257800-139259400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr3:139257800-139259400	Active TSS	Brain Substantia Nigra	brain
33	chr3:139257800-139259400	Active TSS	Duodenum Mucosa	Duodenum
34	chr3:139257800-139259400	Active TSS	Fetal Intestine Large	intestine
35	chr3:139257800-139259600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:139257800-139259600	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:139257800-139259600	Active TSS	NH-A	brain
38	chr3:139257800-139259800	Active TSS	Pancreas	Pancrea
39	chr3:139257800-139259800	Active TSS	HSMMtube	muscle
40	chr3:139258000-139258600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:139258000-139258600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:139258000-139258600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:139258000-139258600	Active TSS	Small Intestine	intestine
44	chr3:139258000-139258800	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr3:139258000-139258800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr3:139258000-139258800	Active TSS	A549	lung
47	chr3:139258000-139259000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:139258000-139259000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:139258000-139259000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:139258000-139259000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links