Variant report

Variant	rs12138940
Chromosome Location	chr1:44974796-44974797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:44965854..44968248-chr1:44973969..44975941,2	K562	blood:
2	chr1:44965779..44967986-chr1:44972874..44975622,2	K562	blood:
3	chr1:44974069..44975867-chr1:45042813..45044583,2	K562	blood:
4	chr1:44971909..44974855-chr1:44979477..44982336,4	K562	blood:
5	chr1:44974401..44976254-chr1:44977179..44979196,2	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]
rs12145658	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];0.95[ASN][1000 genomes]
rs270724	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs72688085	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72688091	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72895565	0.95[ASN][1000 genomes]
rs7550459	1.00[JPT][hapmap];0.95[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
rs12138940	KCNQ4	cis	parietal	SCAN
rs12138940	PTPRF	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:44966200-44975400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:44967600-44975200	Weak transcription	Right Atrium	heart
3	chr1:44968000-44974800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:44971200-44975200	Enhancers	Brain Hippocampus Middle	brain
5	chr1:44971400-44974800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
6	chr1:44971600-44975600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:44972800-44974800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:44973000-44974800	Enhancers	Brain Anterior Caudate	brain
9	chr1:44973200-44977400	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:44973400-44974800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:44973600-44974800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr1:44973800-44974800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr1:44973800-44983000	Enhancers	Brain Substantia Nigra	brain
14	chr1:44974000-44974800	Enhancers	Brain Angular Gyrus	brain
15	chr1:44974000-44975000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:44974000-44975200	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr1:44974400-44975000	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:44974400-44975600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:44974400-44976000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:44974400-44976800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:44974400-44978000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:44974600-44976000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:44974600-44978000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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