Variant report

Variant	rs7620380
Chromosome Location	chr3:158464069-158464070
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:158463959-158464103	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:158461573..158464400-chr3:158464739..158466515,2	K562	blood:
2	chr3:158461553..158464844-chr3:158481750..158486798,5	K562	blood:
3	chr3:158458110..158459848-chr3:158463726..158465479,2	K562	blood:
4	chr3:158458014..158460479-chr3:158462665..158465374,2	MCF-7	breast:
5	chr3:158439350..158441066-chr3:158462153..158464983,2	MCF-7	breast:
6	chr3:158463142..158465142-chr3:158474543..158477563,3	K562	blood:

No data

Variant related genes	Relation type
MFSD1	TF binding region
ENSG00000118855	Chromatin interaction
ENSG00000240207	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1548013	0.92[ASN][1000 genomes]
rs3755746	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680461	1.00[ASN][1000 genomes]
rs4680463	0.89[ASN][1000 genomes]
rs4680466	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61461024	0.94[ASN][1000 genomes]
rs73158358	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7429899	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7616425	0.85[ASN][1000 genomes]
rs7617706	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9290028	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9810241	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9811858	0.96[ASN][1000 genomes]
rs9825140	0.94[ASN][1000 genomes]
rs9849301	0.96[ASN][1000 genomes]
rs9857480	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861289	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7620380	GFM1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450600-158465400	Weak transcription	Left Ventricle	heart
3	chr3:158450800-158464200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:158450800-158468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
6	chr3:158451000-158464400	Weak transcription	NH-A	brain
7	chr3:158451000-158464800	Weak transcription	Gastric	stomach
8	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
10	chr3:158451800-158464800	Weak transcription	Brain Germinal Matrix	brain
11	chr3:158452200-158465600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:158453200-158464600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:158453400-158464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:158453400-158464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:158453400-158465800	Weak transcription	Fetal Brain Female	brain
16	chr3:158453400-158467400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:158453400-158467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:158453600-158465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:158453600-158486400	Weak transcription	Esophagus	oesophagus
20	chr3:158455400-158465800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:158456800-158464800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:158457000-158464600	Weak transcription	HSMM	muscle
23	chr3:158457200-158464800	Weak transcription	Spleen	Spleen
24	chr3:158457200-158468200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:158457400-158486000	Weak transcription	Right Ventricle	heart
26	chr3:158457800-158464800	Weak transcription	Hela-S3	cervix
27	chr3:158457800-158466000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:158457800-158486200	Weak transcription	Pancreas	Pancrea
29	chr3:158458000-158464800	Weak transcription	HSMMtube	muscle
30	chr3:158458000-158471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:158458800-158464600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:158459400-158464800	Weak transcription	Brain Angular Gyrus	brain
33	chr3:158459600-158465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:158459600-158465600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:158459600-158468400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr3:158460000-158468600	Strong transcription	Fetal Intestine Large	intestine
37	chr3:158460200-158466600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:158460400-158464600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:158460400-158465800	Weak transcription	Lung	lung
40	chr3:158460400-158486000	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:158460600-158465600	Weak transcription	Aorta	Aorta
42	chr3:158460800-158469400	Weak transcription	Ovary	ovary
43	chr3:158461000-158464200	Weak transcription	A549	lung
44	chr3:158461000-158464800	Weak transcription	Liver	Liver
45	chr3:158461200-158464800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:158461400-158464200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:158461600-158466800	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:158461600-158468400	Strong transcription	Fetal Intestine Small	intestine
49	chr3:158461600-158468600	Strong transcription	Fetal Stomach	stomach
50	chr3:158462000-158464200	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links