Variant report

Variant	rs3911861
Chromosome Location	chr1:45062453-45062454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45062121..45063093-chr1:45118225..45118785,2	K562	blood:
2	chr1:45060952..45063242-chr1:45097302..45099719,2	K562	blood:
3	chr1:45062445..45064456-chr1:45195206..45197142,2	K562	blood:
4	chr1:45055444..45058536-chr1:45062097..45064282,3	K562	blood:
5	chr1:45062374..45064718-chr1:45079976..45081945,2	K562	blood:

Variant related genes	Relation type
ENSG00000200169	Chromatin interaction
ENSG00000187147	Chromatin interaction

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	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127289	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]
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	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2355360	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378723	0.89[AMR][1000 genomes];0.92[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	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56186608	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59485926	0.82[ASN][1000 genomes]
rs61260531	0.84[ASN][1000 genomes]
rs928685	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[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
rs3911861	ZNF684	cis	cerebellum	SCAN
rs3911861	CCDC24	cis	cerebellum	SCAN
rs3911861	ZSWIM5	cis	parietal	SCAN
rs3911861	TESK2	cis	parietal	SCAN
rs3911861	DMAP1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45018000-45082600	Weak transcription	Right Atrium	heart
2	chr1:45049000-45062800	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr1:45053200-45063600	Enhancers	Brain Hippocampus Middle	brain
4	chr1:45057600-45068800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:45058200-45063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:45058200-45063800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:45060800-45072600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:45061000-45065400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:45061200-45062600	Weak transcription	Brain Anterior Caudate	brain
10	chr1:45061200-45068200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:45062000-45063000	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:45062400-45062600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:45062400-45062600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:45062400-45063400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:45062400-45064800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:45062400-45065400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:45062400-45070600	Enhancers	Brain Substantia Nigra	brain

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