Variant report

Variant	rs3779526
Chromosome Location	chr7:127625636-127625637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127624426..127626535-chr7:127640064..127642521,3	K562	blood:
2	chr7:127624592..127626535-chr7:127640064..127642521,2	K562	blood:
3	chr7:127621276..127623489-chr7:127624505..127626499,2	K562	blood:
4	chr7:127613884..127616731-chr7:127622987..127625650,2	MCF-7	breast:
5	chr7:127622847..127627413-chr7:127635236..127639415,6	K562	blood:
6	chr7:127622034..127626432-chr7:127627902..127631016,5	K562	blood:

Variant related genes	Relation type
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1024910	0.84[ASN][1000 genomes]
rs1193333	0.83[ASN][1000 genomes]
rs1193335	0.84[ASN][1000 genomes]
rs1193336	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs124756	0.83[JPT][hapmap]
rs12668077	0.87[JPT][hapmap]
rs1345509	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419968	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17732677	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs178734	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2241291	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs225241	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs322813	0.83[JPT][hapmap]
rs322819	0.83[JPT][hapmap]
rs322820	0.83[JPT][hapmap]
rs322821	0.83[JPT][hapmap]
rs322823	0.83[JPT][hapmap]
rs322826	0.89[GIH][hapmap];0.83[JPT][hapmap]
rs322827	0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs322828	0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs322831	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs322834	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs322835	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs322836	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs322838	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs322840	0.83[JPT][hapmap]
rs35774036	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757755	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3757760	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3757763	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3779523	0.83[JPT][hapmap]
rs3779527	0.83[ASN][1000 genomes]
rs3808056	0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3808061	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3808077	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3808082	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3808088	0.87[JPT][hapmap]
rs3823995	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4731386	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6467155	0.84[ASN][1000 genomes]
rs6467156	0.84[ASN][1000 genomes]
rs6944446	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs6973092	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7789322	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	27 gene(s)	inside rSNPs	diseases
4	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3779526	TMEM209	cis	cerebellum	SCAN
rs3779526	ARF5	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127583200-127630600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:127587400-127635200	Weak transcription	NHDF-Ad	bronchial
3	chr7:127600600-127630600	Weak transcription	Adipose Nuclei	Adipose
4	chr7:127603000-127627000	Weak transcription	Aorta	Aorta
5	chr7:127607800-127626800	Weak transcription	Ovary	ovary
6	chr7:127609200-127630800	Weak transcription	NH-A	brain
7	chr7:127609400-127635200	Weak transcription	Fetal Kidney	kidney
8	chr7:127614000-127631000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:127614400-127630600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:127617000-127628800	Weak transcription	Spleen	Spleen
11	chr7:127617200-127625800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr7:127617200-127627000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:127617200-127628400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:127617200-127630600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:127617200-127631000	Weak transcription	Esophagus	oesophagus
16	chr7:127617400-127626000	Weak transcription	Brain Hippocampus Middle	brain
17	chr7:127617400-127626600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:127617400-127626800	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:127617400-127627400	Weak transcription	Fetal Brain Male	brain
20	chr7:127617600-127626000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:127617600-127627200	Weak transcription	Brain Anterior Caudate	brain
22	chr7:127617600-127640600	Weak transcription	Brain Germinal Matrix	brain
23	chr7:127618200-127626800	Weak transcription	Fetal Lung	lung
24	chr7:127618200-127633400	Weak transcription	Hela-S3	cervix
25	chr7:127618600-127627000	Weak transcription	Osteobl	bone
26	chr7:127618600-127627600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:127618600-127631200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr7:127618800-127637800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr7:127619000-127630600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:127619400-127631000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:127619400-127631000	Weak transcription	A549	lung
32	chr7:127619600-127625800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:127619600-127626200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr7:127619600-127626600	Weak transcription	Fetal Intestine Large	intestine
35	chr7:127619600-127627000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:127619600-127627000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr7:127619600-127627000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:127619600-127628400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr7:127619600-127628600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:127619600-127628600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr7:127619600-127630000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:127619600-127630200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr7:127619600-127630400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:127619600-127630400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr7:127619600-127630600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:127619600-127630600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:127619600-127630600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:127619600-127630600	Weak transcription	Liver	Liver
49	chr7:127619600-127630600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr7:127619600-127630600	Weak transcription	Dnd41	blood

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