Variant report

Variant	rs1025576
Chromosome Location	chr7:99473624-99473625
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10235630	0.97[ASN][1000 genomes]
rs1048705	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10808114	0.95[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1121592	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs13310903	0.81[ASN][1000 genomes]
rs1865472	0.84[JPT][hapmap]
rs2060452	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082744	0.92[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2082745	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2099446	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2247761	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2247762	0.81[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs2527881	0.93[ASN][1000 genomes]
rs2527886	0.81[MKK][hapmap]
rs2527899	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2527900	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs2527901	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2527902	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs2527903	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2527906	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2527907	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs2527908	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs2527909	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2527911	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527913	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527914	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527915	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527918	0.83[JPT][hapmap]
rs2527919	0.84[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527921	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527922	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2527925	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2527926	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2527927	0.89[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2571991	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2571992	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2571993	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2571994	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2571996	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2571997	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2571998	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2571999	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2572000	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs2572003	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2572005	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2572006	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2572008	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2572009	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]
rs2572010	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2572011	0.81[ASN][1000 genomes]
rs2572012	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2572013	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2572015	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2572018	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2572019	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2572022	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572023	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2572024	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474229	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs533486	0.87[ASW][hapmap]
rs7781442	0.89[CHD][hapmap];0.84[JPT][hapmap]
rs7809747	0.83[AMR][1000 genomes];0.83[EUR][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	nsv966726	chr7:99473527-99488698	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1025576	TRIM4	cis	Artery Aorta	GTEx
rs1025576	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx
rs1025576	TRIM4	cis	cerebellum	SCAN
rs1025576	TRIM4	cis	Stomach	GTEx
rs1025576	OR2AE1	cis	parietal	SCAN
rs1025576	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs1025576	OR2AE1	cis	cerebellum	SCAN
rs1025576	TRIM4	cis	Whole Blood	GTEx
rs1025576	ORAI2	cis	parietal	SCAN
rs1025576	TRIM4	cis	Artery Tibial	GTEx
rs1025576	TRIM4	cis	Adipose Subcutaneous	GTEx
rs1025576	TRIM4	cis	parietal	SCAN
rs1025576	TRIM4	cis	Esophagus Muscularis	GTEx
rs1025576	TRIM4	cis	lesional skin	skin_eQTL
rs1025576	TRIM4	cis	uninvolved skin	skin_eQTL
rs1025576	TRIM4	cis	multi-tissue	Pritchard
rs1025576	TRIM4	cis	Nerve Tibial	GTEx
rs1025576	TRIM4	cis	normal skin	skin_eQTL
rs1025576	TRIM4	cis	Thyroid	GTEx
rs1025576	TRIM4	cis	Muscle Skeletal	GTEx
rs1025576	TRIM4	cis	lung	GTEx
rs1025576	TRIM4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99458200-99489600	Weak transcription	Pancreas	Pancrea
2	chr7:99465200-99475400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:99468400-99487200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:99470000-99489600	Weak transcription	Gastric	stomach
5	chr7:99470400-99486800	Weak transcription	Primary T cells from cord blood	blood
6	chr7:99470400-99487000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:99470600-99474000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:99471400-99487000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:99472000-99473800	Weak transcription	Adipose Nuclei	Adipose
10	chr7:99472400-99487200	Weak transcription	Brain Anterior Caudate	brain
11	chr7:99472400-99487400	Weak transcription	Aorta	Aorta
12	chr7:99472600-99487000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:99472600-99487200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:99472600-99487600	Weak transcription	Lung	lung
15	chr7:99472600-99488800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:99472800-99476200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:99473000-99487200	Weak transcription	Brain Substantia Nigra	brain
18	chr7:99473200-99487200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:99473600-99474600	Enhancers	Primary neutrophils fromperipheralblood	blood

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