Variant report

Variant	rs12127289
Chromosome Location	chr1:45057363-45057364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:44844014..44844555-chr1:45057231..45058074,2	K562	blood:
2	chr1:45031998..45033648-chr1:45056197..45059133,2	K562	blood:
3	chr1:45052900..45054995-chr1:45056850..45058770,2	K562	blood:
4	chr1:45043721..45045810-chr1:45054815..45057693,2	K562	blood:
5	chr1:45050697..45052579-chr1:45054486..45057426,3	K562	blood:
6	chr1:45053495..45055636-chr1:45056850..45058814,2	K562	blood:
7	chr1:45055444..45058536-chr1:45062097..45064282,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10158231	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11211015	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs12068704	0.82[ASN][1000 genomes]
rs12119059	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568345	0.83[JPT][hapmap]
rs12569316	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs16832091	0.92[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1965877	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2355360	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378723	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs270715	0.94[ASN][1000 genomes]
rs270756	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs270768	0.83[JPT][hapmap]
rs3738734	0.83[ASN][1000 genomes]
rs3850851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911861	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56186608	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59485926	0.82[ASN][1000 genomes]
rs61260531	0.84[ASN][1000 genomes]
rs928685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12127289	TESK2	cis	parietal	SCAN
rs12127289	ZNF684	cis	cerebellum	SCAN
rs12127289	ZSWIM5	cis	parietal	SCAN
rs12127289	CCDC24	cis	cerebellum	SCAN
rs12127289	DMAP1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45018000-45082600	Weak transcription	Right Atrium	heart
2	chr1:45047800-45060000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:45049000-45062800	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr1:45050000-45057600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:45052400-45057600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:45053000-45059000	Enhancers	Brain Substantia Nigra	brain
7	chr1:45053200-45063600	Enhancers	Brain Hippocampus Middle	brain
8	chr1:45054200-45057400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:45054200-45057600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:45055400-45061600	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:45055600-45057600	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:45055600-45058000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:45056000-45058200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:45056000-45058400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:45056400-45057600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:45056800-45058200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:45056800-45059200	Enhancers	Brain Anterior Caudate	brain
18	chr1:45057000-45057600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:45057000-45058200	Enhancers	Brain Angular Gyrus	brain
20	chr1:45057000-45058600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:45057200-45057400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr1:45057200-45057400	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr1:45057200-45058400	Enhancers	HSMM	muscle
24	chr1:45057200-45058800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:45057200-45058800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:45057200-45059000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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