Variant report

Variant	rs3929001
Chromosome Location	chr2:54282887-54282888
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	chr2:54281996..54284399-chr2:54289462..54291009,2	MCF-7	breast:
2	chr2:54196526..54198487-chr2:54280269..54283258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10173565	0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs10186140	0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs10201710	0.89[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs10206954	0.89[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs11884229	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11884435	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12615044	0.82[CHB][hapmap]
rs12617094	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs12620359	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs12620667	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12623097	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13399590	0.84[CHB][hapmap];0.87[CHD][hapmap]
rs13417064	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs13425449	0.84[CHB][hapmap]
rs1363060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421618	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs17045536	0.83[CHB][hapmap]
rs1974771	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2112127	0.84[CHB][hapmap]
rs2287640	0.88[CHB][hapmap]
rs2287641	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs2287645	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs58851686	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60191560	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61740458	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545387	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs6713993	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7572559	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs7574376	0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs7583626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7585466	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7593897	0.84[CHB][hapmap]
rs977784	0.89[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3929001	RP11-477N3.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
2	chr2:54268400-54286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:54268400-54290800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:54271400-54286800	Weak transcription	HSMMtube	muscle
5	chr2:54272000-54286600	Weak transcription	HSMM	muscle
6	chr2:54272600-54286600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:54272600-54286800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:54273000-54292400	Weak transcription	Fetal Brain Female	brain
9	chr2:54276800-54286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:54277200-54290800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:54278800-54302400	Weak transcription	Left Ventricle	heart
12	chr2:54280000-54292400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:54280200-54286600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:54280400-54283400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:54280600-54284400	Weak transcription	Liver	Liver
16	chr2:54280800-54283000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:54280800-54283200	Weak transcription	Pancreas	Pancrea
18	chr2:54280800-54285000	Weak transcription	Fetal Intestine Small	intestine
19	chr2:54280800-54286400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:54280800-54286800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:54280800-54291400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:54280800-54310000	Weak transcription	Ovary	ovary
23	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
24	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
26	chr2:54281000-54291200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:54281200-54286600	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:54281200-54292400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:54281600-54286600	Weak transcription	Primary T cells from cord blood	blood
30	chr2:54281600-54289400	Weak transcription	Primary B cells from cord blood	blood
31	chr2:54281600-54308800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:54281800-54284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:54281800-54286600	Weak transcription	Osteobl	bone
34	chr2:54282000-54286800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:54282000-54288400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr2:54282000-54291200	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:54282200-54284800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:54282200-54293800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:54282400-54283200	Weak transcription	Stomach Mucosa	stomach
40	chr2:54282800-54283000	Enhancers	Brain Angular Gyrus	brain
41	chr2:54282800-54283000	Enhancers	Brain Anterior Caudate	brain
42	chr2:54282800-54283600	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:54282800-54283600	Enhancers	Brain Substantia Nigra	brain

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