Variant report

Variant	rs1570916
Chromosome Location	chr6:53851341-53851342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53850945..53851819-chr6:54131033..54131552,2	MCF-7	breast:
2	chr6:53850715..53851537-chr6:54132516..54133234,3	MCF-7	breast:
3	chr6:53850708..53851695-chr6:54108679..54109745,3	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1325825	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs727384	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7765496	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9349689	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9367547	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370251	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382267	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1018062	chr6:53842588-53925192	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1570916	EFHC1	cis	cerebellum	SCAN
rs1570916	C6orf142	cis	cerebellum	SCAN
rs1570916	HCRTR2	cis	cerebellum	SCAN
rs1570916	LRRC1	Cis_1M	lymphoblastoid	RTeQTL
rs1570916	PRIM2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53846400-53852000	Enhancers	HMEC	breast
2	chr6:53846400-53852200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:53847000-53851800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:53847600-53852200	Enhancers	NH-A	brain
5	chr6:53848400-53851800	Weak transcription	Right Ventricle	heart
6	chr6:53849200-53852200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:53849200-53852600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:53849800-53851600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:53849800-53851600	Weak transcription	Left Ventricle	heart
10	chr6:53849800-53851800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:53849800-53852000	Enhancers	Osteobl	bone
12	chr6:53849800-53852200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:53849800-53852200	Enhancers	NHEK	skin
14	chr6:53849800-53853200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:53850200-53851600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:53850200-53851600	Weak transcription	Psoas Muscle	Psoas
17	chr6:53850200-53851800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:53850200-53852200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:53850200-53852600	Enhancers	Fetal Lung	lung
20	chr6:53850400-53851400	Weak transcription	NHDF-Ad	bronchial
21	chr6:53850400-53851600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:53850400-53851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:53850400-53852200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:53850600-53851600	Weak transcription	NHLF	lung
25	chr6:53850600-53853600	Enhancers	Fetal Brain Male	brain
26	chr6:53850800-53852600	Enhancers	Fetal Stomach	stomach
27	chr6:53851000-53852200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:53851000-53852200	Enhancers	HSMM	muscle
29	chr6:53851200-53851400	Enhancers	Colon Smooth Muscle	Colon
30	chr6:53851200-53851400	Active TSS	Stomach Smooth Muscle	stomach
31	chr6:53851200-53851600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr6:53851200-53851600	Active TSS	Brain Anterior Caudate	brain
33	chr6:53851200-53851600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr6:53851200-53851800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr6:53851200-53851800	Enhancers	Brain Hippocampus Middle	brain
36	chr6:53851200-53852000	Enhancers	Fetal Intestine Large	intestine
37	chr6:53851200-53852000	Enhancers	Fetal Intestine Small	intestine
38	chr6:53851200-53852200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:53851200-53852200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr6:53851200-53852200	Enhancers	Liver	Liver
41	chr6:53851200-53852200	Enhancers	HSMMtube	muscle
42	chr6:53851200-53852400	Enhancers	Fetal Heart	heart
43	chr6:53851200-53852600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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