Variant report

Variant	rs8070454
Chromosome Location	chr17:38160754-38160755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38112764..38115622-chr17:38159568..38161737,2	K562	blood:
2	chr17:38149292..38151319-chr17:38159650..38161294,2	K562	blood:
3	chr17:38152599..38155402-chr17:38158806..38161805,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MED24-2	chr17:38159628-38160757	l_1437_chr17:38159627-38161700_breast

Extended variants
information (count: 63 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1042658	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1045929	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11078934	0.84[CEU][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs11655264	0.92[YRI][hapmap]
rs11658328	0.85[YRI][hapmap]
rs11871747	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12600856	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602172	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12941811	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227315	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2227322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2227336	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241245	0.85[YRI][hapmap]
rs2305482	0.82[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap]
rs3213762	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3826331	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3859192	0.81[LWK][hapmap];0.85[MKK][hapmap]
rs3935280	0.83[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs4065321	0.85[LWK][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap]
rs4794822	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4794823	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4794824	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4795412	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4795414	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4795415	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795416	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795418	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795419	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795420	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55771023	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55846942	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56922390	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57065891	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57968500	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59925331	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60082402	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62065177	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6503530	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs709592	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7208815	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7209755	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7214085	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7221894	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7222039	0.97[ASN][1000 genomes]
rs7502514	0.84[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs7502912	0.84[CHD][hapmap]
rs8065443	0.83[CHB][hapmap]
rs8065519	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8066582	0.85[LWK][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap]
rs8067817	0.97[ASN][1000 genomes]
rs8068260	0.92[ASN][1000 genomes]
rs8072548	0.97[ASN][1000 genomes]
rs8073254	0.84[YRI][hapmap]
rs8075668	0.90[MKK][hapmap];0.89[YRI][hapmap]
rs8078723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8081692	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868150	0.83[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap]
rs9303283	0.82[CHB][hapmap];0.85[YRI][hapmap]
rs9915252	0.85[YRI][hapmap]

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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs8070454	PSMD3	cis	multi-tissue	Pritchard
rs8070454	PSMD3	cis	Lymphoblastoid	GTEx
rs8070454	GSDMA	cis	Nerve Tibial	GTEx
rs8070454	MED24	cis	Artery Tibial	GTEx
rs8070454	GSDMA	cis	Esophagus Muscularis	GTEx
rs8070454	MED24	cis	parietal	SCAN
rs8070454	PSMD3	cis	parietal	SCAN
rs8070454	MED24	cis	Thyroid	GTEx
rs8070454	MED24	cis	Nerve Tibial	GTEx
rs8070454	GSDMA	cis	Adipose Subcutaneous	GTEx
rs8070454	MED24	cis	cerebellum	SCAN
rs8070454	MED24	cis	Artery Aorta	GTEx
rs8070454	GSDMA	cis	lung	GTEx
rs8070454	GSDMB	cis	cerebellum	SCAN
rs8070454	PSMD3	cis	Frontal Cortex	GTEx
rs8070454	GSDMA	cis	Artery Aorta	GTEx
rs8070454	PCGF2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38152200-38160800	Weak transcription	K562	blood
2	chr17:38153200-38166400	Weak transcription	Fetal Lung	lung
3	chr17:38153400-38166200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr17:38153400-38166600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:38153800-38166200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:38153800-38166200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr17:38153800-38172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:38154200-38161000	Weak transcription	Lung	lung
9	chr17:38154200-38166400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr17:38154400-38166200	Weak transcription	Dnd41	blood
11	chr17:38154400-38166400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:38154600-38160800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:38154600-38166200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr17:38154600-38166400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:38154600-38170000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:38154600-38170200	Weak transcription	Esophagus	oesophagus
17	chr17:38154800-38173600	Weak transcription	Thymus	Thymus
18	chr17:38155000-38166200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:38155000-38166400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:38155000-38170000	Weak transcription	HSMM	muscle
21	chr17:38155000-38173600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:38155000-38174000	Weak transcription	Fetal Brain Female	brain
23	chr17:38155400-38170200	Weak transcription	Placenta	Placenta
24	chr17:38155600-38164200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:38155600-38166600	Weak transcription	Fetal Thymus	thymus
26	chr17:38155600-38169600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr17:38155600-38169800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:38155800-38161000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:38155800-38171800	Weak transcription	Spleen	Spleen
30	chr17:38160400-38160800	Enhancers	HSMMtube	muscle
31	chr17:38160400-38161200	Enhancers	Fetal Muscle Leg	muscle
32	chr17:38160400-38162000	Enhancers	HepG2	liver
33	chr17:38160600-38160800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr17:38160600-38161000	Enhancers	Stomach Mucosa	stomach
35	chr17:38160600-38161400	Enhancers	Psoas Muscle	Psoas
36	chr17:38160600-38161400	Enhancers	Skeletal Muscle Male	skeletal muscle

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