Variant report

Variant	rs55952713
Chromosome Location	chr6:56815307-56815308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56813824..56816649-chr6:56884972..56886715,2	K562	blood:
2	chr6:56813560..56816424-chr6:56821895..56824578,2	K562	blood:
3	chr6:56786881..56788836-chr6:56814115..56815766,2	MCF-7	breast:
4	chr6:56799165..56801512-chr6:56813694..56816410,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1020548	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193465	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13198484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13207800	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13212013	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13218276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220575	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1451707	0.83[AMR][1000 genomes]
rs1451708	0.83[AMR][1000 genomes]
rs17685277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17685338	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17685380	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2613119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2817573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360535	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34009699	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34027274	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34399458	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34616943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34812189	0.86[AMR][1000 genomes]
rs34979183	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35090265	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35336675	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35434542	0.83[AMR][1000 genomes]
rs35605425	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35735810	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35899012	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35961728	0.83[AMR][1000 genomes]
rs36124814	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56381984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6901944	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6904924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6907143	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6927558	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564870	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564872	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs720884	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7760385	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs55952713	BEND6	cis	Artery Tibial	GTEx
rs55952713	BEND6	cis	Heart Left Ventricle	GTEx
rs55952713	C6orf65	cis	multi-tissue	Pritchard
rs55952713	BEND6	cis	Esophagus Mucosa	GTEx
rs55952713	BEND6	cis	Esophagus Muscularis	GTEx
rs55952713	BEND6	cis	Thyroid	GTEx
rs55952713	BEND6	cis	Muscle Skeletal	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56804200-56818000	Weak transcription	HSMM	muscle
2	chr6:56804400-56815800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:56806600-56817800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:56806600-56818000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:56806600-56818400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:56810000-56818200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:56811400-56815600	Weak transcription	GM12878-XiMat	blood
8	chr6:56812400-56815400	Weak transcription	Brain Anterior Caudate	brain
9	chr6:56812600-56816200	Genic enhancers	Osteobl	bone
10	chr6:56812600-56817400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:56812800-56816000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:56813000-56817400	Weak transcription	Hela-S3	cervix
13	chr6:56813200-56816000	Genic enhancers	NHDF-Ad	bronchial
14	chr6:56813200-56818200	Weak transcription	HSMMtube	muscle
15	chr6:56813400-56815800	Weak transcription	NHEK	skin
16	chr6:56813400-56816200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr6:56813600-56815400	Strong transcription	A549	lung
18	chr6:56813600-56817000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:56813600-56817600	Weak transcription	HMEC	breast
20	chr6:56813800-56816000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:56813800-56816800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:56813800-56816800	Enhancers	NH-A	brain
23	chr6:56814000-56816000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:56814200-56817200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:56814600-56815400	Enhancers	Brain Substantia Nigra	brain
26	chr6:56814600-56815600	Genic enhancers	K562	blood
27	chr6:56814600-56816000	Enhancers	HUVEC	blood vessel
28	chr6:56814600-56818200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:56814800-56815400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:56814800-56815600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:56814800-56815600	Enhancers	Brain Angular Gyrus	brain
32	chr6:56814800-56815800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:56814800-56816200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:56814800-56816200	Enhancers	Brain Cingulate Gyrus	brain
35	chr6:56814800-56818400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:56815000-56815400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:56815000-56815600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr6:56815000-56815800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:56815000-56816000	Enhancers	Brain Hippocampus Middle	brain
40	chr6:56815200-56816200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:56815200-56816600	Enhancers	NHLF	lung
42	chr6:56815200-56818600	Weak transcription	Placenta Amnion	Placenta Amnion

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