Variant report

Variant	rs527731
Chromosome Location	chr13:76345298-76345299
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	chr13:76334673..76336320-chr13:76344020..76346194,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136153	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs474240	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs583368	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs598500	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs658746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs660942	0.91[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs668008	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs674611	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7335067	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9600555	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9600558	1.00[JPT][hapmap]
rs9600561	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs527731	BTF3L1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76323800-76356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:76337400-76347600	Weak transcription	Gastric	stomach
3	chr13:76338000-76356800	Weak transcription	Brain Anterior Caudate	brain
4	chr13:76338000-76362800	Weak transcription	Fetal Stomach	stomach
5	chr13:76338600-76356600	Weak transcription	Left Ventricle	heart
6	chr13:76338800-76371000	Weak transcription	Fetal Thymus	thymus
7	chr13:76339000-76348200	Enhancers	Fetal Intestine Small	intestine
8	chr13:76340000-76363600	Weak transcription	Thymus	Thymus
9	chr13:76340200-76347200	Weak transcription	Pancreas	Pancrea
10	chr13:76340200-76349200	Enhancers	NHDF-Ad	bronchial
11	chr13:76340800-76347200	Enhancers	HepG2	liver
12	chr13:76341200-76346000	Weak transcription	HUVEC	blood vessel
13	chr13:76341800-76352800	Weak transcription	Primary T cells from cord blood	blood
14	chr13:76342000-76346000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr13:76342400-76357800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr13:76343000-76345800	Enhancers	NHLF	lung
17	chr13:76343000-76348200	Enhancers	Fetal Intestine Large	intestine
18	chr13:76343000-76349200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr13:76343200-76345800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:76343200-76346800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:76343400-76346400	Enhancers	Liver	Liver
22	chr13:76343400-76346800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr13:76343400-76347400	Enhancers	Fetal Kidney	kidney
24	chr13:76343400-76347800	Enhancers	HSMMtube	muscle
25	chr13:76343400-76370800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr13:76343600-76346400	Enhancers	Osteobl	bone
27	chr13:76343800-76345600	Flanking Active TSS	A549	lung
28	chr13:76343800-76348400	Genic enhancers	HSMM	muscle
29	chr13:76344000-76345600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr13:76344000-76345800	Enhancers	Stomach Mucosa	stomach
31	chr13:76344000-76346800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr13:76344400-76345600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:76344400-76345800	Enhancers	NH-A	brain
34	chr13:76344400-76346200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr13:76344400-76347400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:76344600-76345600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:76344600-76345600	Enhancers	HMEC	breast
38	chr13:76344600-76346800	Enhancers	Fetal Heart	heart
39	chr13:76344600-76347200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr13:76344600-76347400	Enhancers	NHEK	skin
41	chr13:76344800-76346200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr13:76344800-76346600	Weak transcription	Small Intestine	intestine
43	chr13:76344800-76356800	Weak transcription	Fetal Lung	lung
44	chr13:76345000-76345800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr13:76345000-76346400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr13:76345200-76345400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr13:76345200-76345600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:76345200-76346400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr13:76345200-76346400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr13:76345200-76346400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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