Variant report

Variant	rs10401838
Chromosome Location	chr19:18740353-18740354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18721660..18723951-chr19:18739466..18741646,2	K562	blood:
2	chr19:18738729..18743227-chr19:18745299..18749316,6	K562	blood:
3	chr19:18716086..18718940-chr19:18739610..18741168,2	MCF-7	breast:
4	chr19:18739642..18741715-chr19:18744659..18746767,2	MCF-7	breast:
5	chr19:18725448..18727463-chr19:18738649..18741341,2	K562	blood:

Variant related genes	Relation type
ENSG00000167487	Chromatin interaction
ENSG00000105696	Chromatin interaction
ENSG00000006016	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10402779	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419977	0.88[MEX][hapmap]
rs12459017	0.86[AFR][1000 genomes]
rs12973817	0.98[EUR][1000 genomes]
rs12981028	0.98[EUR][1000 genomes]
rs12983566	0.95[EUR][1000 genomes]
rs3220	0.88[CEU][hapmap]
rs34131922	0.95[EUR][1000 genomes]
rs34863656	0.88[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs35611322	0.98[EUR][1000 genomes]
rs60941598	0.98[EUR][1000 genomes]
rs7256751	1.00[CEU][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8106194	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10401838	FARP1	trans	lymphoblastoid	seeQTL
rs10401838	NDUFA13	cis	parietal	SCAN
rs10401838	CRLF1	cis	parietal	SCAN
rs10401838	PGPEP1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18725600-18747200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr19:18727800-18740400	Weak transcription	Brain Substantia Nigra	brain
3	chr19:18729400-18747200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:18732200-18740600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:18734000-18744200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:18739200-18741200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:18739200-18741200	Enhancers	Brain Germinal Matrix	brain
8	chr19:18739200-18741200	Enhancers	Fetal Brain Male	brain
9	chr19:18739600-18740600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:18739600-18740600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:18739800-18740400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:18739800-18740400	Enhancers	Left Ventricle	heart
13	chr19:18739800-18740600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:18739800-18740600	Enhancers	Lung	lung
15	chr19:18739800-18740800	Enhancers	Brain Anterior Caudate	brain
16	chr19:18739800-18741000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr19:18739800-18741000	Enhancers	Esophagus	oesophagus
18	chr19:18739800-18741200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:18740000-18740400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:18740000-18740400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:18740000-18740800	Enhancers	Brain Hippocampus Middle	brain
22	chr19:18740000-18741200	Enhancers	Adipose Nuclei	Adipose
23	chr19:18740200-18740400	Flanking Active TSS	Fetal Brain Female	brain
24	chr19:18740200-18740400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr19:18740200-18740600	Enhancers	Spleen	Spleen
26	chr19:18740200-18740800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr19:18740200-18744200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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