Variant report

Variant	rs3779389
Chromosome Location	chr7:120444391-120444392
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120443378..120446021-chr7:120589576..120591125,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10252911	0.80[CHB][hapmap]
rs10261886	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs10266755	0.82[CHD][hapmap]
rs17132716	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17143001	0.85[CHB][hapmap]
rs17143009	0.85[CHB][hapmap]
rs17143055	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs1859316	0.80[CHB][hapmap]
rs2107276	0.80[CHB][hapmap]
rs2189452	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3757557	1.00[ASW][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs3779386	0.80[CHB][hapmap]
rs3779387	0.92[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3779388	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3823861	0.86[CHD][hapmap]
rs4141301	1.00[YRI][hapmap]
rs4141309	1.00[ASW][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs41624	0.86[CHD][hapmap]
rs41629	0.86[CHD][hapmap]
rs41632	0.86[CHD][hapmap]
rs4461820	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs58686737	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60837162	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6961583	0.81[ASN][1000 genomes]
rs6971854	0.80[CHB][hapmap]
rs6975372	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs6979247	0.80[CHB][hapmap]
rs73427831	0.82[ASN][1000 genomes]
rs73427834	0.81[ASN][1000 genomes]
rs7776721	0.80[CHB][hapmap]
rs7789807	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3779389	SYCE1	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120423000-120449200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:120425800-120454400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:120427400-120466000	Weak transcription	Fetal Stomach	stomach
5	chr7:120429200-120445600	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:120430400-120468200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:120432600-120444600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:120432600-120453800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:120432600-120455400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:120432600-120468400	Weak transcription	Lung	lung
11	chr7:120433200-120446000	Weak transcription	Fetal Kidney	kidney
12	chr7:120436200-120445600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:120437000-120444800	Weak transcription	Left Ventricle	heart
14	chr7:120438000-120445800	Weak transcription	Liver	Liver
15	chr7:120439000-120445600	Weak transcription	Fetal Heart	heart
16	chr7:120439200-120457800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:120439400-120469200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:120441200-120452600	Weak transcription	Fetal Intestine Small	intestine
19	chr7:120441400-120444600	Weak transcription	Fetal Intestine Large	intestine
20	chr7:120441400-120446400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:120442000-120449600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:120442600-120457400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:120443200-120446400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:120443400-120448600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr7:120443600-120446200	Weak transcription	HUVEC	blood vessel
27	chr7:120443800-120446200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr7:120444000-120444600	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:120444000-120457400	Weak transcription	Adipose Nuclei	Adipose

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