Variant report

Variant	rs3816144
Chromosome Location	chr3:53922620-53922621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53921644..53923214-chr3:53923445..53925751,2	MCF-7	breast:
2	chr3:53914370..53917222-chr3:53919581..53923156,3	MCF-7	breast:
3	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
4	chr3:53919776..53924259-chr3:53924368..53927481,7	K562	blood:
5	chr3:53914339..53916278-chr3:53921868..53924184,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222888	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000113811	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10440151	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046677	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134092	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1157175	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072145	1.00[ASN][1000 genomes]
rs13315972	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982172	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1992155	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083127	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276846	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733073	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3733081	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821867	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4569647	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687757	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687763	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624599	0.93[ASN][1000 genomes]
rs7636856	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893367	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311516	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311518	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822471	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840079	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840362	0.93[ASN][1000 genomes]
rs9869505	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878207	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878562	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs999514	0.97[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3816144	ACTR8	cis	Muscle Skeletal	GTEx
rs3816144	IL17RB	cis	Artery Tibial	GTEx
rs3816144	ACTR8	cis	Thyroid	GTEx
rs3816144	ACTR8	cis	lung	GTEx
rs3816144	RP11-884K10.7	cis	Muscle Skeletal	GTEx
rs3816144	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs3816144	IL17RB	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53916200-53924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:53916200-53924800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:53916600-53923400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:53916600-53924000	Weak transcription	Psoas Muscle	Psoas
5	chr3:53916600-53924000	Weak transcription	A549	lung
6	chr3:53916600-53924400	Weak transcription	Fetal Kidney	kidney
7	chr3:53916600-53924800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:53916600-53924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:53916600-53924800	Weak transcription	Aorta	Aorta
10	chr3:53916800-53923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:53916800-53923200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:53916800-53923400	Weak transcription	Fetal Brain Male	brain
13	chr3:53916800-53924000	Weak transcription	Stomach Mucosa	stomach
14	chr3:53916800-53924400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:53916800-53924600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:53916800-53924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:53917000-53922800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:53917000-53923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:53917200-53922800	Strong transcription	Primary B cells from cord blood	blood
20	chr3:53917200-53922800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:53917200-53923000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:53917200-53923400	Strong transcription	Fetal Intestine Large	intestine
23	chr3:53917400-53923200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:53917600-53922800	Strong transcription	Left Ventricle	heart
25	chr3:53917800-53922800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:53918000-53924800	Weak transcription	Esophagus	oesophagus
27	chr3:53919200-53923200	Weak transcription	Right Ventricle	heart
28	chr3:53919600-53923200	Weak transcription	Brain Angular Gyrus	brain
29	chr3:53919600-53923200	Weak transcription	Brain Anterior Caudate	brain
30	chr3:53919600-53924000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:53919600-53925200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:53920000-53923200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:53920000-53923200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:53920000-53924800	Weak transcription	Lung	lung
35	chr3:53920200-53923800	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:53920200-53924000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:53920200-53924000	Weak transcription	Gastric	stomach
38	chr3:53920200-53924000	Weak transcription	Ovary	ovary
39	chr3:53920200-53924000	Weak transcription	Spleen	Spleen
40	chr3:53920200-53924400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:53920200-53924400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:53920400-53923200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:53920400-53924000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:53920400-53924200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:53920400-53924800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:53920400-53924800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:53920600-53924400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr3:53920800-53922800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
49	chr3:53920800-53923400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:53920800-53924000	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links