Variant report

Variant	rs7555594
Chromosome Location	chr1:56796085-56796086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56791612..56794231-chr1:56795931..56797660,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12030284	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12030407	0.88[EUR][1000 genomes]
rs12043349	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12138574	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4418654	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4442403	0.84[AMR][1000 genomes]
rs4543846	0.84[AMR][1000 genomes]
rs4912176	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4912189	0.81[AMR][1000 genomes]
rs4912324	0.81[AMR][1000 genomes]
rs57354037	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57578827	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60984146	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61772691	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61772727	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61772729	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6677504	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1015037	chr1:56784322-56814739	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7555594	FOXG1	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56782000-56797000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:56787000-56805600	Weak transcription	Left Ventricle	heart
3	chr1:56787200-56800600	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:56788400-56796200	Weak transcription	Psoas Muscle	Psoas
5	chr1:56791200-56820800	Weak transcription	Aorta	Aorta
6	chr1:56792200-56797000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:56792400-56798200	Weak transcription	Ovary	ovary
8	chr1:56793200-56796600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:56793800-56797000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:56794200-56797200	Enhancers	NHLF	lung
11	chr1:56794200-56798000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:56794200-56798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:56794200-56798200	Enhancers	NHDF-Ad	bronchial
14	chr1:56794400-56796400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:56794400-56796600	Enhancers	HepG2	liver
16	chr1:56794400-56797200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:56794400-56797400	Enhancers	Osteobl	bone
18	chr1:56794400-56797800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:56794600-56796400	Enhancers	HSMMtube	muscle
20	chr1:56794600-56798000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:56794600-56798000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:56794600-56798000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:56794800-56797000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:56794800-56797200	Enhancers	Placenta	Placenta
25	chr1:56795000-56797000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:56795200-56797000	Enhancers	GM12878-XiMat	blood
27	chr1:56795400-56796400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:56795400-56796400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr1:56795400-56797000	Enhancers	Liver	Liver
30	chr1:56795400-56797000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:56795400-56797400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:56795400-56797800	Enhancers	Hela-S3	cervix
33	chr1:56795400-56798000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr1:56795400-56798400	Enhancers	Fetal Intestine Small	intestine
35	chr1:56795600-56796400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:56795600-56798000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:56795600-56798200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:56795800-56796400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:56795800-56798200	Enhancers	Fetal Intestine Large	intestine
40	chr1:56796000-56796200	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr1:56796000-56796200	Enhancers	Fetal Heart	heart
42	chr1:56796000-56796400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:56796000-56796400	Enhancers	Fetal Brain Male	brain
44	chr1:56796000-56796600	Enhancers	HUVEC	blood vessel
45	chr1:56796000-56797000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:56796000-56797600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:56796000-56798400	Enhancers	NH-A	brain

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