Variant report

Variant	rs2572009
Chromosome Location	chr7:99489005-99489006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99488840..99491741-chr7:99492480..99496250,3	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10235630	0.81[ASN][1000 genomes]
rs1025576	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1048705	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10808114	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1121592	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13310903	0.86[ASN][1000 genomes]
rs1865472	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2060452	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2082744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2082745	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2099445	0.82[ASN][1000 genomes]
rs2107351	0.84[CHB][hapmap]
rs2247761	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247762	1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527886	0.85[MKK][hapmap]
rs2527899	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527900	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2527901	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527902	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2527903	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2527904	0.94[ASN][1000 genomes]
rs2527906	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527907	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2527908	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2527909	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527911	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527912	0.96[ASN][1000 genomes]
rs2527913	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527914	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527915	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527916	0.97[ASN][1000 genomes]
rs2527918	0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527919	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527920	0.96[ASN][1000 genomes]
rs2527921	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527922	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527925	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527926	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527927	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2571991	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2571992	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571993	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571994	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571995	0.94[ASN][1000 genomes]
rs2571996	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571997	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571998	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571999	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572000	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572002	0.91[ASN][1000 genomes]
rs2572003	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572005	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572006	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572008	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572010	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572011	0.97[ASN][1000 genomes]
rs2572012	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572013	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2572015	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2572018	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2572019	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2572022	0.93[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2572023	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2572024	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4727439	0.96[ASN][1000 genomes]
rs474229	0.93[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs503115	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7781442	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7809747	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	esv1792388	chr7:99468155-99497338	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2572009	TRIM4	cis	lesional skin	skin_eQTL
rs2572009	TRIM4	cis	Muscle Skeletal	GTEx
rs2572009	TRIM4	cis	Thyroid	GTEx
rs2572009	TRIM4	cis	Esophagus Muscularis	GTEx
rs2572009	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2572009	TRIM4	cis	cerebellum	SCAN
rs2572009	OR2AE1	cis	parietal	SCAN
rs2572009	OR2AE1	cis	cerebellum	SCAN
rs2572009	TRIM4	cis	Stomach	GTEx
rs2572009	TRIM4	cis	Whole Blood	GTEx
rs2572009	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2572009	TRIM4	cis	normal skin	skin_eQTL
rs2572009	TRIM4	cis	multi-tissue	Pritchard
rs2572009	TRIM4	cis	uninvolved skin	skin_eQTL
rs2572009	TRIM4	cis	lung	GTEx
rs2572009	TRIM4	cis	Artery Aorta	GTEx
rs2572009	TRIM4	cis	Artery Tibial	GTEx
rs2572009	TRIM4	cis	parietal	SCAN
rs2572009	TRIM4	cis	Esophagus Mucosa	GTEx
rs2572009	TRIM4	cis	Nerve Tibial	GTEx
rs2572009	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2572009	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99458200-99489600	Weak transcription	Pancreas	Pancrea
2	chr7:99470000-99489600	Weak transcription	Gastric	stomach
3	chr7:99479800-99499200	Weak transcription	Small Intestine	intestine
4	chr7:99485200-99499000	Weak transcription	Psoas Muscle	Psoas
5	chr7:99485600-99498200	Weak transcription	NHDF-Ad	bronchial
6	chr7:99485800-99489200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:99485800-99495400	Weak transcription	GM12878-XiMat	blood
8	chr7:99485800-99498200	Weak transcription	HSMMtube	muscle
9	chr7:99485800-99498800	Weak transcription	K562	blood
10	chr7:99486000-99489600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:99486000-99497400	Weak transcription	Esophagus	oesophagus
12	chr7:99486400-99501000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:99486600-99498000	Weak transcription	NH-A	brain
14	chr7:99486800-99490600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:99486800-99491200	Strong transcription	Primary T cells from cord blood	blood
16	chr7:99486800-99498800	Weak transcription	HUVEC	blood vessel
17	chr7:99486800-99499200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:99487000-99489800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:99487000-99490000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:99487000-99490200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:99487000-99490200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:99487000-99490200	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:99487000-99490200	Strong transcription	Fetal Thymus	thymus
24	chr7:99487000-99490400	Strong transcription	Adipose Nuclei	Adipose
25	chr7:99487000-99490400	Strong transcription	Placenta	Placenta
26	chr7:99487000-99490600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:99487000-99490600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:99487000-99490600	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr7:99487000-99490600	Strong transcription	Right Ventricle	heart
30	chr7:99487000-99490600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr7:99487000-99490600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr7:99487200-99489800	Strong transcription	Brain Substantia Nigra	brain
33	chr7:99487200-99490000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:99487200-99490000	Weak transcription	NHEK	skin
35	chr7:99487200-99490200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr7:99487200-99490200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr7:99487200-99490400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:99487200-99490600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr7:99487200-99490600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:99487200-99490600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:99487200-99490600	Strong transcription	Brain Anterior Caudate	brain
42	chr7:99487200-99490600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr7:99487200-99490600	Strong transcription	Brain Hippocampus Middle	brain
44	chr7:99487200-99490600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr7:99487200-99490600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr7:99487200-99490600	Strong transcription	Ovary	ovary
47	chr7:99487200-99490600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:99487400-99490400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:99487400-99490600	Strong transcription	Brain Angular Gyrus	brain
50	chr7:99487400-99490600	Strong transcription	Left Ventricle	heart

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