Variant report

Variant	rs12078593
Chromosome Location	chr1:227507726-227507727
allele	G/T
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:8)
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	chr1:227507662-227507897	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr1:227503213-227507844	SK-N-SH	brain:	n/a	n/a
3	IRF1	chr1:227507594-227507756	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227506036..227507932-chr1:227615818..227619997,3	MCF-7	breast:
2	chr1:227125150..227128196-chr1:227505421..227508280,4	MCF-7	breast:
3	chr1:227438042..227439910-chr1:227506389..227508258,2	K562	blood:
4	chr1:227506797..227508939-chr1:228352123..228354806,2	MCF-7	breast:
5	chr1:227500962..227504758-chr1:227504964..227507747,3	MCF-7	breast:
6	chr1:227456938..227458930-chr1:227506800..227508531,2	K562	blood:
7	chr1:227505544..227508414-chr1:227579779..227582450,2	MCF-7	breast:
8	chr1:227506214..227507997-chr1:227555860..227558711,2	MCF-7	breast:

No data

Variant related genes	Relation type
CDC42BPA	TF binding region
ENSG00000181873	Chromatin interaction
ENSG00000163050	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000234277	Chromatin interaction
ENSG00000242757	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12086059	0.83[AFR][1000 genomes]
rs12089076	1.00[AMR][1000 genomes]
rs16847822	1.00[AMR][1000 genomes]
rs16847912	1.00[AMR][1000 genomes]
rs16847929	1.00[AMR][1000 genomes]
rs16859962	1.00[AMR][1000 genomes]
rs16860227	1.00[AMR][1000 genomes]
rs73088936	1.00[AMR][1000 genomes]
rs73090912	1.00[AMR][1000 genomes]
rs73102372	1.00[AMR][1000 genomes]
rs73102384	1.00[AMR][1000 genomes]
rs73102391	1.00[AMR][1000 genomes]
rs73104364	1.00[AMR][1000 genomes]
rs9919207	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227506800-227510000	Weak transcription	Hela-S3	cervix
2	chr1:227507000-227510200	Weak transcription	Gastric	stomach
3	chr1:227507000-227515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:227507200-227507800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:227507200-227508200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:227507200-227508200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227507200-227508400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:227507200-227508400	Weak transcription	Colonic Mucosa	Colon
9	chr1:227507200-227508400	Enhancers	Fetal Intestine Large	intestine
10	chr1:227507200-227508400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:227507200-227508400	Enhancers	Stomach Mucosa	stomach
12	chr1:227507200-227508600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:227507200-227509000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:227507200-227509200	Enhancers	Brain Anterior Caudate	brain
15	chr1:227507200-227509400	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:227507200-227509800	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:227507200-227510000	Weak transcription	Esophagus	oesophagus
18	chr1:227507200-227510000	Weak transcription	Pancreas	Pancrea
19	chr1:227507200-227510200	Enhancers	Liver	Liver
20	chr1:227507200-227511000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:227507200-227518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:227507400-227507800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:227507400-227508000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr1:227507400-227508200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr1:227507400-227508200	Enhancers	Fetal Brain Male	brain
26	chr1:227507400-227508400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:227507400-227508400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:227507400-227508400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:227507400-227508600	Weak transcription	Fetal Lung	lung
30	chr1:227507400-227508800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:227507400-227508800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:227507400-227509000	Enhancers	Brain Hippocampus Middle	brain
33	chr1:227507400-227509200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:227507400-227509200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:227507400-227510200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:227507400-227510800	Weak transcription	NHEK	skin
37	chr1:227507600-227507800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:227507600-227508200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr1:227507600-227508200	Enhancers	Fetal Kidney	kidney
40	chr1:227507600-227508400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:227507600-227508600	Weak transcription	Brain Angular Gyrus	brain
42	chr1:227507600-227509000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr1:227507600-227510400	Weak transcription	K562	blood

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