Variant report

Variant	rs4653909
Chromosome Location	chr1:228341179-228341180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228291284..228293085-chr1:228340318..228343029,2	K562	blood:
2	chr1:228275698..228278149-chr1:228340202..228341746,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10127705	0.90[EUR][1000 genomes]
rs10495278	0.86[EUR][1000 genomes]
rs10495279	0.86[EUR][1000 genomes]
rs10916266	0.90[EUR][1000 genomes]
rs1094602	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1094603	0.90[EUR][1000 genomes]
rs11577976	0.90[EUR][1000 genomes]
rs11580599	0.86[EUR][1000 genomes]
rs11581169	0.90[EUR][1000 genomes]
rs12034268	0.86[EUR][1000 genomes]
rs12039801	0.86[EUR][1000 genomes]
rs12740965	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1803695	0.90[EUR][1000 genomes]
rs28587961	0.90[EUR][1000 genomes]
rs34687764	0.90[EUR][1000 genomes]
rs3795773	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3795774	0.90[EUR][1000 genomes]
rs41303083	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653906	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653908	0.86[EUR][1000 genomes]
rs4653914	0.86[EUR][1000 genomes]
rs61825156	0.90[EUR][1000 genomes]
rs61825157	0.86[EUR][1000 genomes]
rs61825159	0.86[EUR][1000 genomes]
rs61827462	0.86[EUR][1000 genomes]
rs6663726	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6668719	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530253	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537552	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9287011	0.90[EUR][1000 genomes]
rs9970544	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
8	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
9	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
10	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
11	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised 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	64 gene(s)	inside rSNPs	diseases
13	nsv549290	chr1:228333652-228349806	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv873258	chr1:228334088-228359775	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
15	nsv873259	chr1:228334277-228359775	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
16	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
17	nsv549291	chr1:228338939-228350774	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv873261	chr1:228338939-228359775	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
19	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
20	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
21	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228331400-228341800	Weak transcription	Psoas Muscle	Psoas
2	chr1:228332800-228349800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:228333200-228342200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:228333200-228344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:228333800-228350400	Weak transcription	Primary B cells from cord blood	blood
6	chr1:228336000-228342000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:228336600-228341600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:228336600-228342000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:228336800-228350200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:228337000-228341800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:228337000-228342200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:228337000-228343000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:228337200-228342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:228337200-228344400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:228337400-228343000	Weak transcription	Brain Germinal Matrix	brain
16	chr1:228337600-228343600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:228337800-228341800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:228337800-228342000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:228337800-228342200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:228337800-228343200	Weak transcription	A549	lung
21	chr1:228337800-228349800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:228338000-228342200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:228338000-228343600	Weak transcription	Fetal Brain Female	brain
24	chr1:228338000-228344000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:228338000-228349200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:228338000-228349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:228338200-228342000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:228338200-228342800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:228338200-228344800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:228338200-228344800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:228338200-228352400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:228338400-228349200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:228338600-228343000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:228339000-228344000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:228339000-228346000	Weak transcription	HMEC	breast
36	chr1:228339200-228342000	Weak transcription	NHEK	skin
37	chr1:228339200-228342800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:228339200-228342800	Weak transcription	HSMM	muscle
39	chr1:228339400-228342200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:228339400-228342400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:228339400-228342800	Weak transcription	Osteobl	bone
42	chr1:228339400-228343000	Weak transcription	Stomach Mucosa	stomach
43	chr1:228339400-228343400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:228339400-228344400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:228339400-228344400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:228339400-228345000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:228339400-228352600	Weak transcription	Brain Anterior Caudate	brain
48	chr1:228339600-228341800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:228339600-228342000	Weak transcription	Esophagus	oesophagus
50	chr1:228339600-228342800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links