Variant report

Variant	rs12145658
Chromosome Location	chr1:44978184-44978185
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:44975740..44979460-chr1:44980605..44983213,3	K562	blood:
2	chr1:44974401..44976254-chr1:44977179..44979196,2	K562	blood:
3	chr1:44975674..44978374-chr1:44983451..44986964,3	K562	blood:
4	chr1:44975674..44978843-chr1:44984055..44988124,5	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12122791	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12124022	0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12138940	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12740646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs270724	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs4660811	1.00[YRI][hapmap]
rs72688091	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72895565	1.00[ASN][1000 genomes]
rs7550459	1.00[JPT][hapmap];0.90[ASN][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	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	esv1005212	chr1:44972573-44985674	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12145658	KCNQ4	cis	parietal	SCAN
rs12145658	PTPRF	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44973800-44983000	Enhancers	Brain Substantia Nigra	brain
2	chr1:44974800-44978400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:44975400-44981600	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:44975600-44983000	Enhancers	Brain Hippocampus Middle	brain
5	chr1:44975600-44983200	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr1:44975800-44978200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:44975800-44979400	Enhancers	Brain Angular Gyrus	brain
8	chr1:44976000-44978600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:44976200-44978800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:44976400-44978400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr1:44976400-44985000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:44976800-44978200	Weak transcription	Primary B cells from cord blood	blood
13	chr1:44976800-44978200	Weak transcription	Brain Anterior Caudate	brain
14	chr1:44976800-44978600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr1:44977000-44979600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:44977200-44979000	Bivalent Enhancer	NHEK	skin
17	chr1:44977400-44978600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:44977400-44978800	Enhancers	Primary T cells from cord blood	blood
19	chr1:44977600-44978200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:44977600-44978600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:44977600-44980200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:44977800-44978200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:44977800-44978200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr1:44977800-44978200	Enhancers	Thymus	Thymus
25	chr1:44977800-44978400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
26	chr1:44977800-44978400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:44977800-44978400	Enhancers	Fetal Thymus	thymus
28	chr1:44977800-44978800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:44977800-44983000	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:44978000-44978200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:44978000-44978200	Bivalent Enhancer	Stomach Mucosa	stomach
32	chr1:44978000-44978400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:44978000-44978600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:44978000-44978600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:44978000-44979000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:44978000-44979000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:44978000-44979000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:44978000-44979600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr1:44978000-44980600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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