Variant report

Variant	rs2527901
Chromosome Location	chr7:99525112-99525113
allele	A/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: 77 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1025576	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1048705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10808114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1121592	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12535919	0.82[YRI][hapmap]
rs12536945	0.83[YRI][hapmap]
rs13310903	0.82[ASN][1000 genomes]
rs1865472	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2060452	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2082744	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2082745	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2247761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247762	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2525541	0.85[CHB][hapmap]
rs2525542	0.81[EUR][1000 genomes]
rs2525548	0.85[CHB][hapmap]
rs2527886	0.84[CHB][hapmap]
rs2527890	0.84[CHB][hapmap]
rs2527894	0.84[CHB][hapmap]
rs2527897	0.84[CHB][hapmap]
rs2527899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527900	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527902	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527904	0.97[ASN][1000 genomes]
rs2527906	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2527908	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527909	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527911	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527912	0.96[ASN][1000 genomes]
rs2527913	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527915	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527916	0.97[ASN][1000 genomes]
rs2527918	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527919	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527920	0.96[ASN][1000 genomes]
rs2527921	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527925	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2527926	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2527927	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2571991	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2571992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571993	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571994	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571995	0.97[ASN][1000 genomes]
rs2571996	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571999	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572000	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2572002	0.91[ASN][1000 genomes]
rs2572003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572009	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]
rs2572010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572011	0.94[ASN][1000 genomes]
rs2572012	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2572013	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2572015	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572018	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572019	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572022	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2572023	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2572024	0.81[AMR][1000 genomes]
rs4727439	0.96[ASN][1000 genomes]
rs474229	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs503115	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7781442	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7809747	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2527901	TRIM4	cis	lesional skin	skin_eQTL
rs2527901	TRIM4	cis	uninvolved skin	skin_eQTL
rs2527901	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2527901	TRIM4	cis	multi-tissue	Pritchard
rs2527901	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2527901	TRIM4	cis	Lymphoblastoid	GTEx
rs2527901	TRIM4	cis	normal skin	skin_eQTL
rs2527901	TRIM4	cis	Artery Tibial	GTEx
rs2527901	TRIM4	cis	Artery Aorta	GTEx
rs2527901	TRIM4	cis	Thyroid	GTEx
rs2527901	TRIM4	cis	Muscle Skeletal	GTEx
rs2527901	TRIM4	cis	Whole Blood	GTEx
rs2527901	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2527901	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx
rs2527901	TRIM4	cis	Esophagus Mucosa	GTEx
rs2527901	TRIM4	cis	lung	GTEx
rs2527901	TRIM4	cis	Stomach	GTEx
rs2527901	TRIM4	cis	Esophagus Muscularis	GTEx
rs2527901	TRIM4	cis	Nerve Tibial	GTEx

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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