Variant report

Variant	rs2239801
Chromosome Location	chr3:50402309-50402310
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50402147-50402808	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:50402153-50402451	H1-hESC	embryonic stem cell:	n/a	n/a
3	UBTF	chr3:50402022-50402348	K562	blood:	n/a	n/a
4	ELF1	chr3:50402127-50403089	GM12878	blood:	n/a	n/a
5	TAF1	chr3:50402192-50402409	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr3:50402188-50402388	K562	blood:	n/a	n/a
7	POLR2A	chr3:50402303-50402319	MCF-7	breast:	n/a	n/a
8	MAX	chr3:50401922-50403366	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr3:50402103-50403275	H1-hESC	embryonic stem cell:	n/a	n/a
10	RCOR1	chr3:50402262-50402428	K562	blood:	n/a	n/a
11	E2F6	chr3:50401981-50402380	K562	blood:	n/a	n/a
12	POLR2A	chr3:50402254-50402402	MCF-7	breast:	n/a	n/a
13	CHD2	chr3:50402220-50402466	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr3:50402135-50402652	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3A	chr3:50402202-50403275	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:50402099-50403085	K562	blood:	n/a	n/a
17	MAX	chr3:50401991-50402653	K562	blood:	n/a	n/a
18	BACH1	chr3:50401981-50402425	H1-hESC	embryonic stem cell:	n/a	n/a
19	TBP	chr3:50402085-50402984	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAZ	chr3:50401753-50402997	IMR90	lung:	n/a	n/a
21	POLR2A	chr3:50402229-50402442	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50394074..50395668-chr3:50400374..50402544,2	K562	blood:
2	chr3:50388042..50391116-chr3:50401183..50404211,3	K562	blood:
3	chr3:50392523..50394186-chr3:50400098..50402690,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271858	TF binding region
ENSG00000114395	Chromatin interaction
ENSG00000114388	Chromatin interaction
ENSG00000272104	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10510755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs12629572	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12635953	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1989839	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2071802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2071803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2073498	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2073499	0.93[CEU][hapmap]
rs2233474	0.93[CEU][hapmap]
rs2236939	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2301639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28365992	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3755832	0.91[EUR][1000 genomes]
rs3806708	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4141060	0.93[CEU][hapmap]
rs45536634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57319506	0.88[EUR][1000 genomes]
rs57462170	0.83[EUR][1000 genomes]
rs57838764	0.83[EUR][1000 genomes]
rs58051625	0.86[EUR][1000 genomes]
rs60247651	0.84[EUR][1000 genomes]
rs6776145	1.00[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
12	nsv590256	chr3:50302830-50420554	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
13	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
15	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
16	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
18	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50397800-50402800	Weak transcription	Dnd41	blood
2	chr3:50400000-50402400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:50401600-50402400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr3:50401600-50402400	Genic enhancers	Lung	lung
5	chr3:50401600-50402800	Active TSS	Brain Germinal Matrix	brain
6	chr3:50401800-50402400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:50401800-50402400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:50401800-50402400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:50401800-50402400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:50401800-50402400	Flanking Active TSS	Colonic Mucosa	Colon
11	chr3:50401800-50402400	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr3:50401800-50402800	Active TSS	Fetal Brain Female	brain
13	chr3:50401800-50403000	Active TSS	Primary T cells from cord blood	blood
14	chr3:50401800-50403000	Bivalent Enhancer	Fetal Brain Male	brain
15	chr3:50401800-50403400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:50401800-50403400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr3:50401800-50403400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:50401800-50403800	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:50402000-50402400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:50402000-50402400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:50402000-50402400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:50402000-50402400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:50402000-50402400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:50402000-50402400	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr3:50402000-50402400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr3:50402000-50402400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:50402000-50402400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr3:50402000-50402400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:50402000-50402400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:50402000-50402400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr3:50402000-50402400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:50402000-50402400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:50402000-50402400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:50402000-50402400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:50402000-50402400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:50402000-50402400	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr3:50402000-50402400	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr3:50402000-50402400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:50402000-50402400	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr3:50402000-50402400	Flanking Active TSS	Esophagus	oesophagus
41	chr3:50402000-50402400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr3:50402000-50402400	Flanking Active TSS	Fetal Intestine Large	intestine
43	chr3:50402000-50402400	Flanking Active TSS	Fetal Intestine Small	intestine
44	chr3:50402000-50402400	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr3:50402000-50402400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
46	chr3:50402000-50402400	Flanking Active TSS	Pancreas	Pancrea
47	chr3:50402000-50402400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr3:50402000-50402400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr3:50402000-50402400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr3:50402000-50402400	Flanking Active TSS	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links