Variant report

Variant	rs4075015
Chromosome Location	chr1:154389196-154389197
allele	A/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	CTCF	chr1:154389180-154389330	WERI-Rb-1	eye:	n/a	n/a
2	RUNX3	chr1:154389071-154389521	GM12878	blood:	n/a	n/a
3	EBF1	chr1:154389165-154389572	GM12878	blood:	n/a	chr1:154389369-154389380
4	EBF1	chr1:154389185-154389510	GM12878	blood:	n/a	chr1:154389369-154389380
5	EBF1	chr1:154389174-154389524	GM12878	blood:	n/a	chr1:154389369-154389380
6	RUNX3	chr1:154388994-154389623	GM12878	blood:	n/a	n/a
7	NFIC	chr1:154389027-154389602	GM12878	blood:	n/a	n/a
8	MTA3	chr1:154389131-154389490	GM12878	blood:	n/a	n/a
9	FOXM1	chr1:154389055-154389560	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154376615..154383856-chr1:154388009..154396723,15	MCF-7	breast:
2	chr1:154376358..154381143-chr1:154387661..154394028,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228264	TF binding region
ENSG00000160712	Chromatin interaction
ENSG00000228013	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11265604	0.89[CEU][hapmap]
rs12121085	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs17654071	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs4845612	0.82[EUR][1000 genomes]
rs6692515	0.83[EUR][1000 genomes]
rs72698103	0.81[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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154381000-154390800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:154381000-154390800	Weak transcription	NHLF	lung
3	chr1:154381200-154390800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:154381400-154390400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:154381400-154390600	Weak transcription	NHDF-Ad	bronchial
6	chr1:154381600-154390200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:154381800-154389400	Weak transcription	Colonic Mucosa	Colon
8	chr1:154382000-154390800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:154382000-154390800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:154382400-154391600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:154382600-154390600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:154383000-154390000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:154383400-154389200	Weak transcription	Esophagus	oesophagus
15	chr1:154383400-154389600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:154383400-154390800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:154383600-154391200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:154384200-154389800	Weak transcription	NHEK	skin
19	chr1:154384200-154390000	Weak transcription	HMEC	breast
20	chr1:154384200-154392000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:154384400-154389200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:154384400-154389600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:154384400-154390800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:154385400-154389200	Enhancers	Stomach Smooth Muscle	stomach
25	chr1:154385800-154390600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:154386000-154391000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:154386200-154390600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:154386400-154390600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:154386400-154391200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:154386600-154390800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:154386800-154389200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:154387000-154389600	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:154387000-154390000	Enhancers	Brain Anterior Caudate	brain
34	chr1:154387000-154390800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:154387000-154390800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:154387400-154389200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:154387400-154389200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:154387400-154390400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:154387400-154390800	Weak transcription	Primary T cells from cord blood	blood
40	chr1:154387400-154391000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:154387600-154389200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:154387600-154389600	Weak transcription	Adipose Nuclei	Adipose
43	chr1:154387600-154389600	Weak transcription	Lung	lung
44	chr1:154387600-154389600	Weak transcription	Spleen	Spleen
45	chr1:154387600-154390800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:154387600-154390800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:154387600-154390800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:154387600-154391000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:154387800-154389200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:154387800-154389800	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links