Variant report

Variant	rs72932949
Chromosome Location	chr3:50331225-50331226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50331220-50331351	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:50331023-50331264	K562	blood:	n/a	n/a
3	POLR2A	chr3:50330904-50331325	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:50330669-50331250	ECC-1	luminal epithelium:	n/a	n/a
5	ESRRA	chr3:50328930-50331511	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:50329155-50331254	HepG2	liver:	n/a	n/a
7	TBP	chr3:50331191-50331244	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50329739..50332601-chr3:50372246..50375675,3	MCF-7	breast:
2	chr3:50296030..50318456-chr3:50318822..50339499,66	MCF-7	breast:
3	chr3:50327926..50342388-chr3:50350886..50359960,36	MCF-7	breast:
4	chr3:50305234..50312110-chr3:50326257..50332221,8	MCF-7	breast:
5	chr3:50324564..50342616-chr3:50350801..50362499,49	MCF-7	breast:
6	chr3:50263782..50266098-chr3:50329869..50331619,2	K562	blood:
7	chr3:50315763..50317890-chr3:50327767..50331626,3	K562	blood:
8	chr3:50263477..50265556-chr3:50328393..50331369,3	K562	blood:
9	chr3:50326497..50331702-chr3:50356299..50362839,8	K562	blood:
10	chr3:50327690..50333528-chr3:50363706..50369146,7	MCF-7	breast:

No data

Variant related genes	Relation type
IFRD2	TF binding region
ENSG00000232352	Chromatin interaction
ENSG00000114383	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000068001	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000179564	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17050913	1.00[AMR][1000 genomes]
rs17050922	1.00[AMR][1000 genomes]
rs17050967	0.80[AFR][1000 genomes]
rs57278600	0.82[AFR][1000 genomes]
rs58124375	1.00[AMR][1000 genomes]
rs58407586	1.00[AMR][1000 genomes]
rs59112948	1.00[AMR][1000 genomes]
rs59336516	1.00[AMR][1000 genomes]
rs59896933	1.00[AMR][1000 genomes]
rs60564525	1.00[AMR][1000 genomes]
rs61601450	0.82[AFR][1000 genomes]
rs61638172	1.00[AMR][1000 genomes]
rs72931482	1.00[AMR][1000 genomes]
rs72932915	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932918	1.00[AMR][1000 genomes]
rs72932925	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932994	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934811	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936964	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936978	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938724	1.00[AMR][1000 genomes]
rs72938734	1.00[AMR][1000 genomes]
rs72938735	1.00[AMR][1000 genomes]
rs72938738	1.00[AMR][1000 genomes]
rs72938740	1.00[AMR][1000 genomes]
rs72938750	1.00[AMR][1000 genomes]
rs7611074	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	53 gene(s)	inside rSNPs	diseases
12	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS 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	53 gene(s)	inside rSNPs	diseases
13	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	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
15	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
16	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
17	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
18	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
19	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
20	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
21	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
22	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
23	nsv590257	chr3:50302830-50393640	Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
24	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
25	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
26	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
27	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
28	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

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50330200-50334600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:50330400-50331400	Enhancers	Fetal Brain Male	brain
3	chr3:50330400-50331400	Enhancers	Fetal Thymus	thymus
4	chr3:50330400-50331800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:50330400-50334200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:50330400-50335600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:50330400-50335600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:50330400-50335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:50330400-50335600	Weak transcription	Fetal Lung	lung
10	chr3:50330400-50335800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:50330400-50336000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:50330600-50331400	Enhancers	Adipose Nuclei	Adipose
13	chr3:50330600-50331600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:50330600-50333400	Weak transcription	Brain Germinal Matrix	brain
15	chr3:50330600-50333600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:50330600-50333600	Weak transcription	NHEK	skin
17	chr3:50330600-50333800	Weak transcription	Fetal Brain Female	brain
18	chr3:50330600-50334200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:50330600-50334400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:50330600-50334400	Weak transcription	Placenta	Placenta
21	chr3:50330600-50334400	Weak transcription	NHLF	lung
22	chr3:50330600-50334600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:50330600-50334600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:50330600-50335000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:50330600-50335000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:50330600-50335200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:50330600-50335400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:50330600-50335400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:50330600-50335400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:50330600-50335600	Weak transcription	Primary B cells from cord blood	blood
31	chr3:50330600-50335600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:50330600-50335600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:50330600-50335600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:50330600-50335600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:50330600-50335600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:50330600-50335600	Weak transcription	Thymus	Thymus
37	chr3:50330600-50335600	Weak transcription	HSMM	muscle
38	chr3:50330600-50335600	Weak transcription	HUVEC	blood vessel
39	chr3:50330600-50335600	Weak transcription	Osteobl	bone
40	chr3:50330600-50335800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:50330600-50335800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:50330600-50335800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:50330600-50335800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:50330600-50335800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:50330600-50335800	Weak transcription	Primary T cells from cord blood	blood
46	chr3:50330600-50335800	Weak transcription	Ovary	ovary
47	chr3:50330600-50335800	Weak transcription	Right Atrium	heart
48	chr3:50330600-50335800	Weak transcription	A549	lung
49	chr3:50330600-50335800	Weak transcription	NHDF-Ad	bronchial
50	chr3:50330800-50333000	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links