Variant report

Variant	rs2236219
Chromosome Location	chr1:45101478-45101479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45101174-45102014	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:45100935-45101506	K562	blood:	n/a	n/a
3	POLR2A	chr1:45100312-45102002	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45082233..45083943-chr1:45100424..45103474,3	MCF-7	breast:
2	chr1:45081882..45083718-chr1:45100175..45102916,2	MCF-7	breast:
3	chr1:45100500..45107773-chr1:45184365..45188884,11	K562	blood:
4	chr1:45100964..45102855-chr1:45141535..45143464,3	K562	blood:
5	chr1:45100701..45102574-chr1:45138081..45139709,2	K562	blood:
6	chr1:45100850..45102792-chr17:56735332..56737862,2	MCF-7	breast:
7	chr1:45091834..45094647-chr1:45100049..45102686,2	MCF-7	breast:
8	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:
9	chr1:45100621..45102600-chr1:45195327..45197896,2	K562	blood:

No data

Variant related genes	Relation type
RNF220	TF binding region
ENSG00000198520	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000187147	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1051664	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs11581074	1.00[CHB][hapmap]
rs11584765	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11588956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355365	0.82[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs28453885	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3444	0.82[TSI][hapmap]
rs3768439	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs3850853	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap]
rs4660284	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4660285	0.82[EUR][1000 genomes]
rs4660818	0.81[CHD][hapmap]
rs4660821	0.81[CHD][hapmap]
rs6429544	0.92[CHB][hapmap]
rs6667593	0.92[CHB][hapmap]
rs6683133	0.84[CHD][hapmap]
rs72671954	0.81[EUR][1000 genomes]
rs7538419	0.84[CHD][hapmap]
rs7539312	1.00[CHB][hapmap]
rs995089	0.84[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45098400-45103400	Genic enhancers	Esophagus	oesophagus
2	chr1:45098400-45116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:45098600-45102000	Genic enhancers	Brain Inferior Temporal Lobe	brain
4	chr1:45098800-45101800	Genic enhancers	Brain Hippocampus Middle	brain
5	chr1:45098800-45103800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:45099000-45101600	Genic enhancers	Brain Angular Gyrus	brain
7	chr1:45099000-45101600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
8	chr1:45099000-45102000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:45099000-45102000	Genic enhancers	Brain Substantia Nigra	brain
10	chr1:45099000-45102000	Strong transcription	HSMMtube	muscle
11	chr1:45099000-45102200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:45099000-45103600	Genic enhancers	Fetal Brain Female	brain
13	chr1:45099000-45103800	Genic enhancers	Spleen	Spleen
14	chr1:45099000-45104200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:45099000-45108600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
16	chr1:45099000-45111400	Genic enhancers	Colon Smooth Muscle	Colon
17	chr1:45099000-45115600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:45099000-45116800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr1:45099000-45117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:45099000-45117800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:45099200-45101800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:45099200-45102600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:45099200-45105400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:45099200-45108600	Strong transcription	Aorta	Aorta
25	chr1:45099200-45109200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:45099200-45111400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:45099200-45117600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:45099200-45118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:45099400-45103400	Strong transcription	HMEC	breast
30	chr1:45099400-45106800	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr1:45099400-45107000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:45099400-45108200	Strong transcription	A549	lung
33	chr1:45099400-45110600	Strong transcription	Osteobl	bone
34	chr1:45099400-45115000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:45099400-45115600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:45099400-45117200	Strong transcription	Placenta	Placenta
37	chr1:45099400-45120800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:45099400-45121000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:45099400-45121200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:45099600-45101600	Strong transcription	Rectal Smooth Muscle	rectum
41	chr1:45099600-45102600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:45099600-45110200	Strong transcription	NHLF	lung
43	chr1:45099600-45110400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:45099600-45114600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:45099600-45115400	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr1:45099600-45115600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:45099600-45117200	Strong transcription	Primary B cells from cord blood	blood
48	chr1:45099600-45117200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr1:45099600-45118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:45099600-45118800	Strong transcription	Fetal Thymus	thymus

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