Variant report

Variant	rs3965330
Chromosome Location	chr5:177049442-177049443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10036396	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10040391	0.89[ASN][1000 genomes]
rs10063842	0.84[ASN][1000 genomes]
rs1047577	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12654617	0.87[ASN][1000 genomes]
rs13164561	0.89[ASN][1000 genomes]
rs17832583	0.80[ASN][1000 genomes]
rs1872623	0.92[ASN][1000 genomes]
rs1963011	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2133716	0.87[ASN][1000 genomes]
rs2334991	0.83[ASN][1000 genomes]
rs2650285	0.85[ASN][1000 genomes]
rs28375402	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34327383	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4458584	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56981142	0.84[ASN][1000 genomes]
rs59542146	0.81[ASN][1000 genomes]
rs6882209	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6886539	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6889184	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7703727	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7708299	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7731783	0.87[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	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3965330	RP11-1101H11.1	cis	Heart Left Ventricle	GTEx
rs3965330	RP11-1277A3.2	cis	Nerve Tibial	GTEx
rs3965330	B4GALT7	cis	Whole Blood	GTEx
rs3965330	FAM153A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028600-177053200	Weak transcription	HSMM	muscle
2	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
3	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:177035000-177051000	Weak transcription	Stomach Mucosa	stomach
5	chr5:177035000-177054200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:177035200-177053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:177037000-177055200	Weak transcription	NHLF	lung
8	chr5:177038600-177054400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:177039400-177051400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:177041600-177050200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:177041600-177054400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr5:177043400-177050000	Strong transcription	Ovary	ovary
13	chr5:177043400-177052800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:177043600-177051800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:177043800-177049800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:177044000-177051400	Weak transcription	HMEC	breast
17	chr5:177044400-177050000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:177044400-177061800	Weak transcription	Small Intestine	intestine
19	chr5:177044600-177049800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr5:177045000-177050200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:177045000-177054200	Weak transcription	GM12878-XiMat	blood
22	chr5:177046000-177052600	Weak transcription	Fetal Intestine Small	intestine
23	chr5:177046400-177055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:177046400-177058800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:177046600-177049600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr5:177046600-177049800	Weak transcription	NHEK	skin
27	chr5:177046600-177050000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:177046600-177051400	Weak transcription	Left Ventricle	heart
29	chr5:177046600-177053200	Weak transcription	HSMMtube	muscle
30	chr5:177046600-177054400	Weak transcription	Right Ventricle	heart
31	chr5:177046600-177055000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:177046600-177068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:177046600-177069200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:177046600-177069600	Weak transcription	Esophagus	oesophagus
35	chr5:177046800-177051200	Weak transcription	Fetal Thymus	thymus
36	chr5:177046800-177051200	Weak transcription	Spleen	Spleen
37	chr5:177046800-177054000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:177046800-177054200	Weak transcription	Brain Anterior Caudate	brain
39	chr5:177046800-177054400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:177046800-177058800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr5:177046800-177060200	Weak transcription	Brain Angular Gyrus	brain
42	chr5:177046800-177060800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:177046800-177065800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:177046800-177084000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:177047000-177049800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr5:177047000-177051200	Weak transcription	Aorta	Aorta
47	chr5:177047000-177051600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:177047000-177052400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:177047000-177054200	Weak transcription	Fetal Brain Male	brain
50	chr5:177047000-177055600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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