Variant report

Variant	rs2236390
Chromosome Location	chr1:95776788-95776789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RWDD3-1	chr1:95776726-95776836	NONHSAT004658

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12403330	0.84[AMR][1000 genomes]
rs17113351	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113357	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113362	0.82[AFR][1000 genomes]
rs17113368	0.88[CEU][hapmap]
rs17113369	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs17113372	0.82[AFR][1000 genomes]
rs56854428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968523	0.84[AFR][1000 genomes]
rs9729952	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830648	chr1:95760162-95926264	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1006113	chr1:95768502-96139003	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2236390	GFI1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95769200-95782000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:95772800-95777400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:95773800-95778200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:95774400-95786800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:95774600-95776800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:95774600-95778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:95775000-95778000	Enhancers	Fetal Brain Female	brain
8	chr1:95775400-95776800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:95776000-95777600	Enhancers	Fetal Brain Male	brain
10	chr1:95776400-95777200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:95776400-95777200	Weak transcription	Brain Germinal Matrix	brain
12	chr1:95776400-95777400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:95776400-95777400	Enhancers	Fetal Heart	heart
14	chr1:95776600-95776800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:95776600-95777000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:95776600-95777000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:95776600-95777000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:95776600-95777000	Weak transcription	Fetal Kidney	kidney
19	chr1:95776600-95777200	Enhancers	H9 Cell Line	embryonic stem cell
20	chr1:95776600-95777200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:95776600-95777200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:95776600-95777200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:95776600-95777200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:95776600-95777400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:95776600-95777400	Enhancers	Fetal Lung	lung

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