Variant report

Variant	rs1046014
Chromosome Location	chr5:7859434-7859435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:7859050..7861346-chr5:7868691..7871781,3	MCF-7	breast:
2	chr5:7849544..7853202-chr5:7856682..7860407,3	K562	blood:
3	chr5:7856634..7862841-chr5:7863423..7866521,7	MCF-7	breast:
4	chr5:7857476..7859602-chr5:7864063..7866187,3	K562	blood:
5	chr5:7858641..7861141-chr5:7867787..7870622,3	K562	blood:

Variant related genes	Relation type
ENSG00000215217	Chromatin interaction
ENSG00000124279	Chromatin interaction
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10380	0.93[CEU][hapmap];0.80[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs10520874	0.94[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12347	0.80[CHD][hapmap]
rs162026	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162028	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs162035	0.80[CHD][hapmap]
rs162036	0.85[MEX][hapmap]
rs162131	0.85[MEX][hapmap]
rs16879305	0.93[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16879356	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16879410	0.81[CEU][hapmap]
rs2277958	0.85[EUR][1000 genomes]
rs2303079	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2303081	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs326118	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs326210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs327581	0.80[CHD][hapmap]
rs3776454	0.84[EUR][1000 genomes]
rs41282639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4702507	0.94[CEU][hapmap];0.80[CHD][hapmap]
rs56219526	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57937475	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61536869	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72716534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72716536	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332	0.80[CHD][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1046014	FASTKD3	Cis_1M	lymphoblastoid	RTeQTL
rs1046014	MTRR	cis	lymphoblastoid	seeQTL
rs1046014	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs1046014	MTRR	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7851200-7859600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:7851400-7859600	Weak transcription	Esophagus	oesophagus
3	chr5:7851400-7860000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:7851600-7859800	Weak transcription	Psoas Muscle	Psoas
5	chr5:7851600-7859800	Weak transcription	Right Ventricle	heart
6	chr5:7851600-7860000	Weak transcription	Aorta	Aorta
7	chr5:7851600-7861600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:7851600-7861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:7851600-7865000	Weak transcription	Small Intestine	intestine
10	chr5:7851600-7866400	Weak transcription	Fetal Heart	heart
11	chr5:7851800-7859600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:7851800-7861800	Weak transcription	Brain Substantia Nigra	brain
13	chr5:7851800-7868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:7852200-7867600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:7852200-7868400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:7852200-7868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:7852200-7868400	Weak transcription	Gastric	stomach
18	chr5:7852200-7868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:7852400-7859600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:7852400-7859800	Weak transcription	Spleen	Spleen
21	chr5:7852400-7861000	Weak transcription	HepG2	liver
22	chr5:7852400-7867800	Weak transcription	Fetal Brain Male	brain
23	chr5:7852800-7862000	Weak transcription	Lung	lung
24	chr5:7852800-7868400	Weak transcription	Pancreas	Pancrea
25	chr5:7853400-7860000	Weak transcription	Fetal Intestine Small	intestine
26	chr5:7853400-7861800	Weak transcription	Ovary	ovary
27	chr5:7853400-7862200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:7853600-7859600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:7854000-7861800	Weak transcription	HUVEC	blood vessel
30	chr5:7854000-7868400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:7855200-7859600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:7855200-7859600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:7855400-7859600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:7855600-7860800	Weak transcription	Colonic Mucosa	Colon
35	chr5:7856000-7860800	Weak transcription	NHEK	skin
36	chr5:7856000-7868400	Weak transcription	Stomach Mucosa	stomach
37	chr5:7856400-7859800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:7856600-7867600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:7856800-7860200	Weak transcription	NHLF	lung
40	chr5:7857000-7861200	Strong transcription	Fetal Stomach	stomach
41	chr5:7857200-7859600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:7857600-7860400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:7857600-7860600	Strong transcription	Brain Cingulate Gyrus	brain
44	chr5:7857600-7860600	Strong transcription	Fetal Kidney	kidney
45	chr5:7857600-7862800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:7857600-7863200	Strong transcription	Brain Hippocampus Middle	brain
47	chr5:7857600-7864200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:7857600-7867800	Strong transcription	Fetal Muscle Leg	muscle
49	chr5:7857800-7859600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr5:7857800-7862400	Strong transcription	Left Ventricle	heart

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