Variant report

Variant	rs13316695
Chromosome Location	chr3:49684917-49684918
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49576104..49578514-chr3:49684857..49687792,2	MCF-7	breast:
2	chr3:49683730..49686310-chr3:49694623..49697344,2	K562	blood:
3	chr3:49676360..49678118-chr3:49683625..49686002,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1060962	0.81[ASN][1000 genomes]
rs11130212	0.97[ASN][1000 genomes]
rs11130213	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1131095	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11709525	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710037	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718165	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720597	0.83[AMR][1000 genomes]
rs11917431	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919311	0.87[ASN][1000 genomes]
rs11921590	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13064576	0.86[AMR][1000 genomes]
rs13085791	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352890	0.92[ASN][1000 genomes]
rs1873625	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873626	0.92[ASN][1000 genomes]
rs2005557	0.81[ASN][1000 genomes]
rs2131104	0.81[ASN][1000 genomes]
rs2172252	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329020	0.92[ASN][1000 genomes]
rs2960548	0.87[ASN][1000 genomes]
rs3197999	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34762726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007338	0.92[ASN][1000 genomes]
rs35404120	0.92[ASN][1000 genomes]
rs4283605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855847	0.92[ASN][1000 genomes]
rs4855852	0.87[ASN][1000 genomes]
rs4855881	0.87[ASN][1000 genomes]
rs4855884	0.81[ASN][1000 genomes]
rs6765869	0.81[ASN][1000 genomes]
rs6770670	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803222	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614725	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9812791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822268	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823546	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9824092	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827708	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833611	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836291	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837341	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837520	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9858542	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	0.83[AMR][1000 genomes]
rs9882740	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13316695	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs13316695	FAM212A	cis	Muscle Skeletal	GTEx
rs13316695	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:49661600-49692400	Weak transcription	Ovary	ovary
3	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
4	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:49673800-49692400	Weak transcription	Gastric	stomach
6	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:49676000-49686400	Weak transcription	Spleen	Spleen
8	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
9	chr3:49676400-49687000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:49679600-49687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:49679800-49687600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:49681000-49685400	Weak transcription	Fetal Stomach	stomach
13	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:49682000-49685200	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:49682200-49689000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:49682600-49688400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:49683000-49687000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:49683200-49685200	Weak transcription	Brain Germinal Matrix	brain
20	chr3:49683200-49686000	Enhancers	Brain Angular Gyrus	brain
21	chr3:49683200-49686600	Enhancers	Pancreas	Pancrea
22	chr3:49684400-49685000	Weak transcription	Liver	Liver
23	chr3:49684400-49685800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:49684600-49685000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:49684600-49685600	Enhancers	Primary hematopoietic stem cells	blood
26	chr3:49684600-49686000	Enhancers	Adipose Nuclei	Adipose
27	chr3:49684600-49686000	Enhancers	Brain Anterior Caudate	brain
28	chr3:49684600-49686600	Enhancers	Right Atrium	heart
29	chr3:49684600-49687400	Enhancers	Fetal Heart	heart
30	chr3:49684600-49687800	Genic enhancers	Brain Inferior Temporal Lobe	brain
31	chr3:49684800-49685000	Enhancers	Fetal Brain Female	brain
32	chr3:49684800-49685000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr3:49684800-49685800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:49684800-49686000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:49684800-49687400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:49684800-49687400	Enhancers	Left Ventricle	heart
37	chr3:49684800-49687600	Enhancers	Psoas Muscle	Psoas
38	chr3:49684800-49688000	Enhancers	HepG2	liver
39	chr3:49684800-49688400	Enhancers	Fetal Muscle Leg	muscle
40	chr3:49684800-49688800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:49684800-49689400	Enhancers	Fetal Muscle Trunk	muscle

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