Variant report

Variant	rs1931564
Chromosome Location	chr1:94597160-94597161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94596499..94598702-chr1:94606759..94609677,2	K562	blood:
2	chr1:94586639..94589043-chr1:94594789..94597259,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198691	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10493869	0.86[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10493870	0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10874835	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165076	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165079	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165080	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165082	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11588391	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025221	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12035820	0.81[AMR][1000 genomes]
rs17111122	0.86[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs1931566	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1931570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789439	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3789440	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3789442	0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3789443	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3789444	0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3789445	0.90[TSI][hapmap]
rs3827714	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147798	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147801	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61784007	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61784009	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv871416	chr1:94566311-94635028	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv870932	chr1:94579053-94607607	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv871679	chr1:94579426-94598568	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv871502	chr1:94579426-94607607	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv871306	chr1:94579426-94609478	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv871210	chr1:94579426-94629643	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1931564	FAM69A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94595600-94598000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:94595800-94597600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:94596400-94597200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:94596400-94597400	Enhancers	HSMMtube	muscle
5	chr1:94596600-94597200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:94596600-94597200	Enhancers	HepG2	liver
7	chr1:94596600-94597200	Enhancers	NHLF	lung
8	chr1:94596600-94597200	Flanking Active TSS	Osteobl	bone
9	chr1:94596600-94597400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:94596600-94597400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:94596600-94597400	Enhancers	HSMM	muscle
12	chr1:94596600-94597400	Enhancers	NHDF-Ad	bronchial
13	chr1:94596600-94597600	Enhancers	Placenta	Placenta
14	chr1:94596600-94598000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:94596600-94598000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:94596800-94597200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:94596800-94597200	Enhancers	Liver	Liver
18	chr1:94596800-94597200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:94596800-94597400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:94596800-94598000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:94596800-94599000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:94597000-94597200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:94597000-94597200	Enhancers	Spleen	Spleen
24	chr1:94597000-94597600	Enhancers	NH-A	brain
25	chr1:94597000-94598000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:94597000-94598200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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