Variant report

Variant	rs1561266
Chromosome Location	chr2:113287964-113287965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113285064..113288834-chr2:113298277..113302791,7	MCF-7	breast:
2	chr2:113287458..113289198-chr2:113298107..113300239,2	MCF-7	breast:
3	chr2:113284781..113289468-chr2:113295871..113300752,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POLR1B-2	chr2:113286258-113289988	NONHSAT073697

Variant related genes	Relation type
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11679929	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987434	1.00[ASN][1000 genomes]
rs12988536	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13025468	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1465817	0.93[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34047777	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263686	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34364366	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892661	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086865	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961916	0.93[CEU][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849070	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs62158651	1.00[ASN][1000 genomes]
rs6707618	0.86[CEU][hapmap]
rs6708841	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708927	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs67178025	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726169	0.86[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729910	0.85[CEU][hapmap]
rs6757757	0.85[CEU][hapmap]
rs6759275	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs71414672	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414673	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7506	0.80[ASW][hapmap];0.88[LWK][hapmap]
rs7570679	0.86[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573493	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586685	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589793	0.87[EUR][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	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1561266	RGPD8	cis	Adipose Subcutaneous	GTEx
rs1561266	RGPD8	cis	Whole Blood	GTEx
rs1561266	RGPD8	cis	lung	GTEx
rs1561266	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs1561266	RGPD8	cis	Nerve Tibial	GTEx
rs1561266	RGPD8	cis	Muscle Skeletal	GTEx
rs1561266	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs1561266	RGPD8	cis	Esophagus Muscularis	GTEx
rs1561266	RGPD8	cis	Artery Aorta	GTEx
rs1561266	RGPD8	cis	Artery Tibial	GTEx
rs1561266	RGPD8	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
2	chr2:113260800-113298800	Weak transcription	Fetal Heart	heart
3	chr2:113267400-113290000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:113270600-113298800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:113277800-113290000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:113279000-113299200	Weak transcription	Psoas Muscle	Psoas
7	chr2:113280200-113288800	Weak transcription	K562	blood
8	chr2:113281200-113299000	Weak transcription	Colonic Mucosa	Colon
9	chr2:113284800-113291200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:113285600-113291400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:113285800-113288800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:113285800-113289800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr2:113285800-113289800	Strong transcription	Ovary	ovary
14	chr2:113285800-113289800	Strong transcription	NHDF-Ad	bronchial
15	chr2:113285800-113290400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:113285800-113290600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:113285800-113290800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:113285800-113291200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:113285800-113291200	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:113285800-113291200	Strong transcription	Thymus	Thymus
21	chr2:113285800-113291200	Strong transcription	Osteobl	bone
22	chr2:113285800-113291400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:113285800-113291400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:113285800-113291400	Strong transcription	Dnd41	blood
25	chr2:113285800-113291600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:113285800-113291600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:113286000-113288000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:113286000-113288000	Strong transcription	HUVEC	blood vessel
29	chr2:113286000-113288400	Genic enhancers	Brain Hippocampus Middle	brain
30	chr2:113286000-113289600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr2:113286000-113290000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:113286000-113291000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:113286000-113291200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:113286000-113291400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:113286000-113291400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:113286000-113291400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:113286000-113291400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:113286000-113291400	Strong transcription	Fetal Thymus	thymus
39	chr2:113286000-113291400	Strong transcription	Left Ventricle	heart
40	chr2:113286000-113291600	Strong transcription	Fetal Stomach	stomach
41	chr2:113286000-113291600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr2:113286000-113292200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:113286000-113292200	Strong transcription	Fetal Brain Female	brain
44	chr2:113286200-113288000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:113286200-113288000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:113286200-113288200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:113286200-113288200	Genic enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:113286200-113288200	Strong transcription	Right Ventricle	heart
49	chr2:113286200-113288200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:113286200-113288200	Strong transcription	A549	lung

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