Variant report

Variant	rs2527902
Chromosome Location	chr7:99525071-99525072
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	chr7:99523651..99525447-chr7:99527733..99529553,2	MCF-7	breast:
2	chr7:99524861..99526650-chr7:99605841..99607428,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10235630	0.86[EUR][1000 genomes]
rs1025576	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs1048705	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10808114	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1121592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310903	0.81[ASN][1000 genomes]
rs1865472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060452	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2082744	0.94[JPT][hapmap]
rs2099445	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2099446	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2247761	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2247762	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527881	0.86[EUR][1000 genomes]
rs2527899	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527901	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527903	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527906	0.97[ASN][1000 genomes]
rs2527907	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2527908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527909	0.97[ASN][1000 genomes]
rs2527911	0.96[ASN][1000 genomes]
rs2527912	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527913	0.96[ASN][1000 genomes]
rs2527914	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527915	0.96[ASN][1000 genomes]
rs2527916	0.97[ASN][1000 genomes]
rs2527918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527919	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527920	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527921	0.96[ASN][1000 genomes]
rs2527922	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527926	0.91[ASN][1000 genomes]
rs2527927	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2571991	0.91[ASN][1000 genomes]
rs2571992	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2571993	0.97[ASN][1000 genomes]
rs2571994	0.97[ASN][1000 genomes]
rs2571995	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571996	0.97[ASN][1000 genomes]
rs2571997	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2571998	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2571999	0.96[ASN][1000 genomes]
rs2572000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572002	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2572003	0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572005	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572006	0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572008	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2572009	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2572010	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2572011	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2572012	0.91[ASN][1000 genomes]
rs2572013	0.90[ASN][1000 genomes]
rs2572019	0.94[JPT][hapmap]
rs2572022	0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs2572023	0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs4727439	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474229	0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap]
rs7781442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809747	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2527902	TRIM4	cis	Artery Tibial	GTEx
rs2527902	TRIM4	cis	lesional skin	skin_eQTL
rs2527902	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2527902	OR2AE1	cis	parietal	SCAN
rs2527902	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2527902	TRIM4	cis	multi-tissue	Pritchard
rs2527902	TRIM4	cis	Thyroid	GTEx
rs2527902	PILRB	cis	parietal	SCAN
rs2527902	TRIM4	cis	normal skin	skin_eQTL
rs2527902	ORAI2	cis	parietal	SCAN
rs2527902	TRIM4	cis	uninvolved skin	skin_eQTL
rs2527902	OR2AE1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99517600-99526800	Weak transcription	Gastric	stomach
2	chr7:99517800-99526600	Weak transcription	Esophagus	oesophagus
3	chr7:99517800-99526600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr7:99518000-99526600	Weak transcription	Fetal Stomach	stomach
5	chr7:99518200-99525800	Weak transcription	Adipose Nuclei	Adipose
6	chr7:99518200-99526600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:99518200-99526800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:99518200-99526800	Weak transcription	Brain Anterior Caudate	brain
9	chr7:99518200-99526800	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:99518200-99527000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:99518200-99527000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr7:99518400-99526800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:99518400-99526800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:99518600-99526400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr7:99519600-99526200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:99519800-99526800	Weak transcription	HSMM	muscle
17	chr7:99524400-99526200	Enhancers	HepG2	liver
18	chr7:99524400-99526600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:99524400-99526800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:99524800-99526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:99525000-99526800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:99525000-99526800	Weak transcription	HMEC	breast

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