Variant report

Variant	rs1060472
Chromosome Location	chr4:57259465-57259466
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57256994..57259922-chr4:57269239..57271312,2	K562	blood:
2	chr4:57252534..57255192-chr4:57257421..57260881,3	MCF-7	breast:
3	chr4:57257925..57261959-chr4:57299598..57302953,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAICS-3	chr4:57253640-57259528	NONHSAT096500

Variant related genes	Relation type
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000269921	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10008223	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10013402	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10017460	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10051	0.81[ASN][1000 genomes]
rs10434444	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10434445	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10461357	0.85[ASN][1000 genomes]
rs11133442	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11133443	0.89[TSI][hapmap]
rs1124569	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12498340	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12501334	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501502	1.00[CEU][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12503412	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12504291	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12505939	0.81[ASN][1000 genomes]
rs12508008	0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs12509542	0.83[ASN][1000 genomes]
rs12510712	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12511770	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12513091	0.83[ASN][1000 genomes]
rs12646703	0.88[MEX][hapmap]
rs12646890	0.83[ASN][1000 genomes]
rs13147900	0.95[JPT][hapmap]
rs1356787	0.88[MEX][hapmap]
rs1401904	0.95[JPT][hapmap]
rs1401906	0.95[JPT][hapmap]
rs14211	0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs1474179	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1520026	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1520030	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17086696	0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17086794	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17086832	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17086853	0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs1967559	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1983378	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2030366	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2271923	1.00[CEU][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28510634	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28866881	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796541	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3796548	0.89[TSI][hapmap]
rs4263445	0.88[ASN][1000 genomes]
rs4340842	0.95[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4346704	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4493603	1.00[CEU][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4618376	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4864579	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4864580	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4864583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4865088	0.88[ASN][1000 genomes]
rs4865089	0.89[ASN][1000 genomes]
rs4865092	0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4865103	0.85[ASN][1000 genomes]
rs4865107	0.83[ASN][1000 genomes]
rs4865108	0.81[ASN][1000 genomes]
rs5010012	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55915354	0.81[ASN][1000 genomes]
rs56040009	0.81[ASN][1000 genomes]
rs56099714	0.83[ASN][1000 genomes]
rs56392224	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56887793	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58151706	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61032900	0.88[ASN][1000 genomes]
rs6554345	0.95[JPT][hapmap]
rs6554358	0.86[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs6584	0.88[MEX][hapmap]
rs66810706	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66858948	0.88[ASN][1000 genomes]
rs66863699	0.83[ASN][1000 genomes]
rs67957495	0.88[ASN][1000 genomes]
rs6820279	0.88[ASN][1000 genomes]
rs6820314	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6821301	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6824893	0.80[ASN][1000 genomes]
rs6829250	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6830518	0.88[MEX][hapmap]
rs6832797	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6834696	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834736	0.95[JPT][hapmap]
rs6836118	0.89[TSI][hapmap]
rs6846895	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6849183	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap];0.84[YRI][hapmap];0.88[EUR][1000 genomes]
rs7664841	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7670991	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7696808	0.86[TSI][hapmap];0.85[YRI][hapmap]
rs8340	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9799864	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1060472	SRP72	cis	cerebellum	SCAN
rs1060472	AASDH	cis	parietal	SCAN
rs1060472	SRP72	cis	Esophagus Mucosa	GTEx
rs1060472	SRP72	cis	parietal	SCAN
rs1060472	SRP72	cis	Adipose Subcutaneous	GTEx
rs1060472	SRP72	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57268400	Weak transcription	Lung	lung
3	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
4	chr4:57254600-57264000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:57254600-57271600	Weak transcription	Ovary	ovary
6	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
7	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:57254800-57260800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:57254800-57261800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:57254800-57262000	Weak transcription	Placenta	Placenta
11	chr4:57254800-57264000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:57254800-57264000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:57254800-57271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
19	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
20	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:57255000-57260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:57255000-57261200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:57255000-57262200	Weak transcription	A549	lung
24	chr4:57255000-57264400	Weak transcription	Brain Germinal Matrix	brain
25	chr4:57255000-57264800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:57255000-57265600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:57255000-57266000	Weak transcription	Primary B cells from cord blood	blood
28	chr4:57255000-57266200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:57255000-57266200	Weak transcription	NH-A	brain
30	chr4:57255000-57266400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr4:57255000-57266400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:57255000-57266600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:57255000-57266600	Weak transcription	HSMM	muscle
34	chr4:57255000-57266800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:57255000-57269200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:57255000-57271400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:57255200-57262000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:57255200-57262200	Weak transcription	Fetal Lung	lung
39	chr4:57255200-57262200	Weak transcription	Osteobl	bone
40	chr4:57255200-57264000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:57255200-57264000	Weak transcription	Fetal Stomach	stomach
42	chr4:57255200-57266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:57255200-57266200	Weak transcription	HUVEC	blood vessel
44	chr4:57255200-57266400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr4:57255200-57266800	Weak transcription	Fetal Kidney	kidney
46	chr4:57255200-57266800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:57255200-57267200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:57255200-57267400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:57255200-57271600	Weak transcription	NHEK	skin
50	chr4:57255200-57272200	Weak transcription	Stomach Smooth Muscle	stomach

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