Variant report

Variant	rs326210
Chromosome Location	chr5:7857582-7857583
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:7816149..7817026-chr5:7856829..7857627,3	MCF-7	breast:
2	chr5:7856421..7858362-chr5:7867413..7869187,3	MCF-7	breast:
3	chr5:7762117..7763085-chr5:7856695..7857660,8	MCF-7	breast:
4	chr5:7849544..7853202-chr5:7856682..7860407,3	K562	blood:
5	chr5:7853828..7855824-chr5:7856209..7859029,2	K562	blood:
6	chr5:7856634..7862841-chr5:7863423..7866521,7	MCF-7	breast:
7	chr5:7826263..7828308-chr5:7856719..7858613,3	K562	blood:
8	chr5:7856190..7858153-chr5:7870591..7872655,2	K562	blood:
9	chr5:7857476..7859602-chr5:7864063..7866187,3	K562	blood:

No data

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

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1046014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10520874	0.80[CEU][hapmap]
rs12347	0.95[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs161870	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs161871	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs162026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162034	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs162035	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs162036	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs162039	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs162131	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2303079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs326118	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326125	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs327581	0.89[CEU][hapmap]
rs327592	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41282639	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61536869	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72716534	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72716536	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

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
rs326210	MTRR	cis	Lymphoblastoid	GTEx
rs326210	MTRR	cis	multi-tissue	Pritchard
rs326210	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs326210	PFDN5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 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	chr5:7851400-7857800	Weak transcription	Left Ventricle	heart
3	chr5:7851400-7858000	Weak transcription	HSMM	muscle
4	chr5:7851400-7859600	Weak transcription	Esophagus	oesophagus
5	chr5:7851400-7860000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:7851600-7857600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:7851600-7857600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:7851600-7857600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:7851600-7857600	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:7851600-7857800	Weak transcription	Brain Angular Gyrus	brain
11	chr5:7851600-7857800	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:7851600-7857800	Weak transcription	Fetal Intestine Large	intestine
13	chr5:7851600-7858000	Weak transcription	Adipose Nuclei	Adipose
14	chr5:7851600-7858200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:7851600-7859000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:7851600-7859200	Weak transcription	Fetal Brain Female	brain
17	chr5:7851600-7859800	Weak transcription	Psoas Muscle	Psoas
18	chr5:7851600-7859800	Weak transcription	Right Ventricle	heart
19	chr5:7851600-7860000	Weak transcription	Aorta	Aorta
20	chr5:7851600-7861600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:7851600-7861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:7851600-7865000	Weak transcription	Small Intestine	intestine
23	chr5:7851600-7866400	Weak transcription	Fetal Heart	heart
24	chr5:7851800-7857800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:7851800-7859200	Weak transcription	HMEC	breast
26	chr5:7851800-7859600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr5:7851800-7861800	Weak transcription	Brain Substantia Nigra	brain
28	chr5:7851800-7868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:7852000-7857600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:7852200-7858000	Weak transcription	A549	lung
31	chr5:7852200-7858200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr5:7852200-7867600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:7852200-7868400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:7852200-7868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:7852200-7868400	Weak transcription	Gastric	stomach
36	chr5:7852200-7868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:7852400-7857600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:7852400-7859600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:7852400-7859800	Weak transcription	Spleen	Spleen
40	chr5:7852400-7861000	Weak transcription	HepG2	liver
41	chr5:7852400-7867800	Weak transcription	Fetal Brain Male	brain
42	chr5:7852600-7857600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:7852600-7857600	Weak transcription	Fetal Muscle Leg	muscle
44	chr5:7852600-7858000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:7852600-7858600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr5:7852800-7857600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:7852800-7857600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:7852800-7858000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr5:7852800-7858000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:7852800-7858200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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