Variant report

Variant	rs1465817
Chromosome Location	chr2:113286492-113286493
allele	A/T
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	chr2:113284781..113287040-chr2:113297336..113301005,3	K562	blood:
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: 28 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11679929	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987434	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12988536	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13025468	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs1561266	0.93[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34047777	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263686	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34364366	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892661	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086865	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961916	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158651	1.00[ASN][1000 genomes]
rs6707618	1.00[ASW][hapmap];0.93[CEU][hapmap]
rs6708841	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708927	0.93[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67178025	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726169	0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729910	0.92[CEU][hapmap]
rs6757757	0.92[CEU][hapmap]
rs6759275	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs71414672	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570679	0.93[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573493	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589793	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1465817	RGPD8	cis	Muscle Skeletal	GTEx
rs1465817	RGPD8	cis	lung	GTEx
rs1465817	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs1465817	RGPD8	cis	Thyroid	GTEx
rs1465817	RGPD8	cis	Esophagus Muscularis	GTEx
rs1465817	RGPD8	cis	Adipose Subcutaneous	GTEx
rs1465817	RGPD8	cis	Nerve Tibial	GTEx
rs1465817	RGPD8	cis	Whole Blood	GTEx
rs1465817	RGPD8	cis	Artery Aorta	GTEx
rs1465817	RGPD8	cis	Artery Tibial	GTEx
rs1465817	LOC653596	cis	multi-tissue	Pritchard
rs1465817	RGPD8	cis	Esophagus Mucosa	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	chr2:113272600-113287400	Weak transcription	Fetal Kidney	kidney
6	chr2:113277600-113287400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:113277800-113290000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:113279000-113299200	Weak transcription	Psoas Muscle	Psoas
9	chr2:113280200-113288800	Weak transcription	K562	blood
10	chr2:113281200-113299000	Weak transcription	Colonic Mucosa	Colon
11	chr2:113284800-113291200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:113285600-113291400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:113285800-113286600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:113285800-113287800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:113285800-113288800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:113285800-113289800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr2:113285800-113289800	Strong transcription	Ovary	ovary
18	chr2:113285800-113289800	Strong transcription	NHDF-Ad	bronchial
19	chr2:113285800-113290400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:113285800-113290600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:113285800-113290800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:113285800-113291200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:113285800-113291200	Strong transcription	Fetal Muscle Leg	muscle
24	chr2:113285800-113291200	Strong transcription	Thymus	Thymus
25	chr2:113285800-113291200	Strong transcription	Osteobl	bone
26	chr2:113285800-113291400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:113285800-113291400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:113285800-113291400	Strong transcription	Dnd41	blood
29	chr2:113285800-113291600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:113285800-113291600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:113286000-113286600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr2:113286000-113287000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:113286000-113287000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:113286000-113287800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:113286000-113288000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:113286000-113288000	Strong transcription	HUVEC	blood vessel
37	chr2:113286000-113288400	Genic enhancers	Brain Hippocampus Middle	brain
38	chr2:113286000-113289600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr2:113286000-113290000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:113286000-113291000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:113286000-113291200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:113286000-113291400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:113286000-113291400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:113286000-113291400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:113286000-113291400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr2:113286000-113291400	Strong transcription	Fetal Thymus	thymus
47	chr2:113286000-113291400	Strong transcription	Left Ventricle	heart
48	chr2:113286000-113291600	Strong transcription	Fetal Stomach	stomach
49	chr2:113286000-113291600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr2:113286000-113292200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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