Variant report

Variant	rs2572023
Chromosome Location	chr7:99474427-99474428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10235630	0.99[ASN][1000 genomes]
rs1025576	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]
rs1048705	0.81[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10808114	0.83[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs1121592	0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs1865472	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2060452	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2082744	0.81[CEU][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs2082745	0.80[AMR][1000 genomes]
rs2099446	0.81[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs2247761	0.81[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2247762	0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2527881	0.95[ASN][1000 genomes]
rs2527899	0.81[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs2527900	0.88[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs2527901	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2527902	0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs2527903	0.81[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2527907	0.81[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2527908	0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs2527912	0.81[ASN][1000 genomes]
rs2527914	0.81[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2527916	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2527918	0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2527919	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2527920	0.81[ASN][1000 genomes]
rs2527922	0.81[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2527926	0.85[ASN][1000 genomes]
rs2527927	0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2571992	0.81[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2571997	0.81[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2571998	0.81[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2572000	0.88[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2572003	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs2572005	0.81[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2572006	0.81[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap]
rs2572008	0.81[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2572009	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]
rs2572010	0.81[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2572011	0.82[ASN][1000 genomes]
rs2572012	0.85[ASN][1000 genomes]
rs2572013	0.84[ASN][1000 genomes]
rs2572019	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs2572022	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2572024	0.99[ASN][1000 genomes]
rs4727439	0.81[ASN][1000 genomes]
rs474229	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs503115	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7781442	0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.81[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	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2572023	TRIM4	cis	Nerve Tibial	GTEx
rs2572023	TRIM4	cis	lesional skin	skin_eQTL
rs2572023	OR2AE1	cis	parietal	SCAN
rs2572023	TRIM4	cis	Esophagus Muscularis	GTEx
rs2572023	TRIM4	cis	Muscle Skeletal	GTEx
rs2572023	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2572023	TRIM4	cis	normal skin	skin_eQTL
rs2572023	TRIM4	cis	uninvolved skin	skin_eQTL
rs2572023	OR2AE1	cis	cerebellum	SCAN
rs2572023	TRIM4	cis	multi-tissue	Pritchard
rs2572023	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2572023	TRIM4	cis	Thyroid	GTEx
rs2572023	ORAI2	cis	parietal	SCAN
rs2572023	TRIM4	cis	lung	GTEx
rs2572023	TRIM4	cis	Artery Tibial	GTEx
rs2572023	PILRB	cis	parietal	SCAN
rs2572023	TRIM4	cis	Artery Aorta	GTEx
rs2572023	SPAG1	trans	cerebellum	SCAN
rs2572023	PILRB	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 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	chr7:99471400-99487000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:99472400-99487200	Weak transcription	Brain Anterior Caudate	brain
9	chr7:99472400-99487400	Weak transcription	Aorta	Aorta
10	chr7:99472600-99487000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:99472600-99487200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:99472600-99487600	Weak transcription	Lung	lung
13	chr7:99472600-99488800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:99472800-99476200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:99473000-99487200	Weak transcription	Brain Substantia Nigra	brain
16	chr7:99473200-99487200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:99473600-99474600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr7:99473800-99474600	Strong transcription	Adipose Nuclei	Adipose
19	chr7:99474000-99474600	Bivalent Enhancer	K562	blood
20	chr7:99474000-99475400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:99474200-99474600	Enhancers	Esophagus	oesophagus

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