Variant report

Variant	rs56075263
Chromosome Location	chr3:158364333-158364334
allele	A/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:5)
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	chr3:158364045-158364351	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:158362024..158365390-chr3:158367743..158370169,5	MCF-7	breast:
2	chr3:158362317..158363897-chr3:158363962..158367298,3	MCF-7	breast:
3	chr17:74732561..74734850-chr3:158362272..158364719,2	MCF-7	breast:
4	chr3:158361174..158366807-chr3:158367896..158374332,10	K562	blood:
5	chr3:158284750..158291147-chr3:158359832..158364955,8	K562	blood:

No data

Variant related genes	Relation type
GFM1	TF binding region
ENSG00000178053	Chromatin interaction
ENSG00000168827	Chromatin interaction
ENSG00000161547	Chromatin interaction
ENSG00000243150	Chromatin interaction
ENSG00000207556	Chromatin interaction
ENSG00000092931	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs17630607	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17630980	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17642769	0.80[AMR][1000 genomes]
rs17643171	0.80[AMR][1000 genomes]
rs17697458	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17698494	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17699103	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17699324	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17699478	0.80[AMR][1000 genomes]
rs17699526	0.82[AMR][1000 genomes]
rs2279561	0.80[AMR][1000 genomes]
rs2279562	0.80[AMR][1000 genomes]
rs2304408	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2307064	0.82[AMR][1000 genomes]
rs28372852	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35057010	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3867391	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55666734	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56089835	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56148431	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56167308	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56242377	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60942689	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62286647	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62286649	0.83[ASN][1000 genomes]
rs62286650	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62286654	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62287938	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62288301	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62288303	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62288305	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62288306	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62288307	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62288344	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62288345	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776901	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777231	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804230	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7610009	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7628497	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633713	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	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
6	esv3399089	chr3:158356055-158410094	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs56075263	GFM1	cis	Thyroid	GTEx
rs56075263	LXN	cis	multi-tissue	Pritchard
rs56075263	GFM1	cis	Artery Tibial	GTEx
rs56075263	GFM1	cis	Muscle Skeletal	GTEx
rs56075263	GFM1	cis	Esophagus Mucosa	GTEx
rs56075263	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs56075263	LXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158362800-158367600	Weak transcription	Spleen	Spleen
2	chr3:158362800-158369800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:158362800-158389600	Weak transcription	Gastric	stomach
4	chr3:158362800-158389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:158362800-158390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:158363000-158364600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:158363000-158364600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:158363000-158364800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:158363000-158364800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:158363000-158364800	Enhancers	Brain Angular Gyrus	brain
11	chr3:158363000-158365800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:158363000-158366200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:158363000-158367800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:158363000-158369800	Weak transcription	Aorta	Aorta
15	chr3:158363000-158369800	Weak transcription	Lung	lung
16	chr3:158363000-158370400	Weak transcription	Pancreas	Pancrea
17	chr3:158363000-158376600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:158363000-158378200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:158363000-158379800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:158363000-158381800	Weak transcription	Esophagus	oesophagus
21	chr3:158363200-158364400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:158363200-158364400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:158363200-158364600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:158363200-158370200	Weak transcription	Colonic Mucosa	Colon
25	chr3:158363200-158378600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:158363200-158389400	Weak transcription	Fetal Brain Male	brain
27	chr3:158363400-158364400	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:158363400-158364800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:158363400-158365400	Weak transcription	Fetal Thymus	thymus
30	chr3:158363400-158367000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:158363400-158367200	Weak transcription	Right Ventricle	heart
32	chr3:158363400-158367400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:158363400-158367600	Weak transcription	Stomach Mucosa	stomach
34	chr3:158363400-158369800	Weak transcription	Small Intestine	intestine
35	chr3:158363400-158370400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:158363400-158374200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:158363400-158376600	Weak transcription	Fetal Kidney	kidney
38	chr3:158363600-158364400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:158363600-158364400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:158363600-158364400	Enhancers	Fetal Brain Female	brain
41	chr3:158363600-158364400	Genic enhancers	HMEC	breast
42	chr3:158363600-158364600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:158363600-158364600	Enhancers	Stomach Smooth Muscle	stomach
44	chr3:158363600-158364800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:158363600-158364800	Genic enhancers	HUVEC	blood vessel
46	chr3:158363600-158365200	Strong transcription	HSMM	muscle
47	chr3:158363600-158366200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:158363600-158367200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:158363600-158367600	Weak transcription	Fetal Stomach	stomach
50	chr3:158363600-158367600	Weak transcription	HSMMtube	muscle

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