Variant report

Variant	rs72698115
Chromosome Location	chr1:154379369-154379370
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	MTA3	chr1:154379260-154380836	GM12878	blood:	n/a	n/a
2	IKZF1	chr1:154378840-154380430	GM12878	blood:	n/a	n/a
3	FOS	chr1:154378432-154379516	MCF10A-Er-Src	breast:	n/a	chr1:154378725-154378736 chr1:154378751-154378761 chr1:154378751-154378761 chr1:154378725-154378737 chr1:154378727-154378735 chr1:154378751-154378761 chr1:154378726-154378736
4	POLR2A	chr1:154379014-154380354	GM12892	blood:	n/a	n/a
5	SPI1	chr1:154379265-154380593	GM12878	blood:	n/a	chr1:154380459-154380472 chr1:154379949-154379958
6	POLR2A	chr1:154377491-154380860	MCF10A-Er-Src	breast:	n/a	n/a
7	RUNX3	chr1:154378008-154380714	GM12878	blood:	n/a	n/a
8	CHD1	chr1:154376982-154381411	IMR90	lung:	n/a	n/a
9	MAZ	chr1:154376864-154379687	IMR90	lung:	n/a	chr1:154378849-154378860 chr1:154378850-154378859
10	NFIC	chr1:154379302-154380385	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:154377502-154382614	MCF10A-Er-Src	breast:	n/a	n/a
12	FOXM1	chr1:154379316-154380449	GM12878	blood:	n/a	n/a
13	MXI1	chr1:154377096-154381012	IMR90	lung:	n/a	n/a
14	RELA	chr1:154379234-154380331	GM18951	blood:	n/a	n/a
15	RUNX3	chr1:154379322-154381160	GM12878	blood:	n/a	n/a
16	CTCF	chr1:154379240-154379390	HPF	lung:	n/a	n/a
17	MTA3	chr1:154378011-154380656	GM12878	blood:	n/a	n/a
18	PML	chr1:154378788-154381090	GM12878	blood:	n/a	n/a
19	STAT5A	chr1:154379285-154380426	GM12878	blood:	n/a	chr1:154380008-154380020 chr1:154379949-154379960
20	POLR2A	chr1:154377097-154381240	GM18505	blood:	n/a	n/a
21	EBF1	chr1:154379353-154380218	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:154377291-154381193	IMR90	lung:	n/a	n/a
23	RCOR1	chr1:154376980-154381066	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154377039..154379691-chr1:154908164..154910149,2	MCF-7	breast:
2	chr1:154296377..154299135-chr1:154376809..154380119,3	MCF-7	breast:
3	chr1:154378359..154380579-chr1:154401148..154402901,2	MCF-7	breast:
4	chr1:154154370..154156741-chr1:154377003..154381011,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	TF binding region
ENSG00000163344	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000160712	Chromatin interaction
ENSG00000270361	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11265608	0.96[EUR][1000 genomes]
rs12026876	0.96[EUR][1000 genomes]
rs12033701	0.96[EUR][1000 genomes]
rs1209264	0.82[EUR][1000 genomes]
rs2481065	0.82[EUR][1000 genomes]
rs58548028	0.86[EUR][1000 genomes]
rs72696301	0.96[EUR][1000 genomes]
rs73026617	0.96[EUR][1000 genomes]
rs9651036	0.96[EUR][1000 genomes]
rs9651053	0.96[EUR][1000 genomes]
rs9651055	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers 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	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers 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 target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154377000-154381000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr1:154377000-154381200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:154377200-154379400	Active TSS	Esophagus	oesophagus
4	chr1:154377200-154380400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:154377200-154381200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:154377400-154379400	Active TSS	Left Ventricle	heart
7	chr1:154377400-154379400	Active TSS	Psoas Muscle	Psoas
8	chr1:154377400-154379600	Active TSS	Right Ventricle	heart
9	chr1:154377400-154379800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:154377400-154379800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:154377400-154380800	Flanking Active TSS	HMEC	breast
12	chr1:154377400-154381200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:154377600-154379400	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:154377600-154379400	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr1:154377600-154379400	Active TSS	Right Atrium	heart
16	chr1:154377600-154379400	Active TSS	NHDF-Ad	bronchial
17	chr1:154377600-154379600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr1:154377600-154379800	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr1:154377600-154380400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:154377800-154379400	Active TSS	Small Intestine	intestine
21	chr1:154377800-154380400	Active TSS	Liver	Liver
22	chr1:154377800-154381200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:154378000-154379400	Bivalent/Poised TSS	Thymus	Thymus
24	chr1:154378000-154381200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr1:154378200-154379400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr1:154378200-154379800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:154378200-154379800	Flanking Active TSS	Placenta	Placenta
28	chr1:154378200-154380400	Flanking Active TSS	Colonic Mucosa	Colon
29	chr1:154378200-154380600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:154378200-154381000	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr1:154378200-154381000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:154378200-154381400	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:154378200-154382600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr1:154378400-154379400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:154378400-154380600	Enhancers	Fetal Heart	heart
36	chr1:154378400-154380800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:154378400-154381200	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr1:154378600-154379400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:154378600-154379400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr1:154378600-154379400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:154378600-154379600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:154378600-154379600	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr1:154378600-154379800	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr1:154378600-154380600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:154378600-154381000	Flanking Active TSS	NHEK	skin
46	chr1:154378800-154379400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
47	chr1:154378800-154379400	Active TSS	Primary T cells fromperipheralblood	blood
48	chr1:154378800-154379600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:154378800-154379800	Flanking Active TSS	Hela-S3	cervix
50	chr1:154378800-154380600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links