Variant report

Variant	rs7609717
Chromosome Location	chr3:158412942-158412943
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1038886	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1047366	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10936158	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12496174	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13074694	0.80[ASN][1000 genomes]
rs13324770	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13325932	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1602760	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1864503	0.86[AMR][1000 genomes]
rs1864507	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2303909	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28481597	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3845272	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4680449	0.82[AMR][1000 genomes]
rs4680450	0.88[AMR][1000 genomes]
rs4680451	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4680452	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4680453	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4680457	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441212	0.82[AMR][1000 genomes]
rs6441220	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6772483	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6781342	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6802317	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7621897	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7653826	0.82[AMR][1000 genomes]
rs8455	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs891464	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9819567	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9824985	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7609717	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs7609717	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs7609717	MLF1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390400-158416800	Weak transcription	Aorta	Aorta
2	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:158390600-158427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:158390800-158416800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:158390800-158425400	Weak transcription	Fetal Brain Female	brain
6	chr3:158390800-158427000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:158390800-158427400	Weak transcription	Esophagus	oesophagus
8	chr3:158390800-158427400	Weak transcription	Lung	lung
9	chr3:158390800-158429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:158390800-158430200	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:158390800-158430400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
13	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
14	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
15	chr3:158390800-158444200	Weak transcription	Gastric	stomach
16	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:158391000-158413600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:158391000-158418600	Weak transcription	Fetal Brain Male	brain
19	chr3:158391000-158421000	Weak transcription	Fetal Heart	heart
20	chr3:158391000-158427200	Weak transcription	NHEK	skin
21	chr3:158391000-158427400	Weak transcription	Pancreas	Pancrea
22	chr3:158391000-158429200	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:158391000-158430600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:158395800-158420800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:158395800-158423000	Weak transcription	Fetal Stomach	stomach
27	chr3:158396200-158418400	Weak transcription	Brain Germinal Matrix	brain
28	chr3:158396800-158413800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:158397000-158429200	Weak transcription	Ovary	ovary
30	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
32	chr3:158397800-158425200	Weak transcription	HSMMtube	muscle
33	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:158400600-158429000	Weak transcription	Brain Substantia Nigra	brain
35	chr3:158403200-158413000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:158403600-158438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:158403800-158420800	Weak transcription	HMEC	breast
38	chr3:158408000-158417800	Strong transcription	Fetal Intestine Large	intestine
39	chr3:158408400-158413000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:158408400-158430200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr3:158408400-158443000	Weak transcription	HepG2	liver
42	chr3:158408600-158419400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:158408800-158422400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:158409000-158429800	Weak transcription	Small Intestine	intestine
45	chr3:158409200-158421200	Weak transcription	Psoas Muscle	Psoas
46	chr3:158409200-158427400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:158409400-158414400	Weak transcription	NHLF	lung
48	chr3:158409400-158415200	Weak transcription	NH-A	brain
49	chr3:158409400-158425400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:158409400-158425600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links