Variant report

Variant	rs7579230
Chromosome Location	chr2:54690939-54690940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54682049..54684426-chr2:54689582..54692090,2	MCF-7	breast:
2	chr2:54686513..54688620-chr2:54689845..54691769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10169422	0.85[ASN][1000 genomes]
rs10200103	1.00[ASN][1000 genomes]
rs12713258	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988330	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988767	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990140	0.97[ASN][1000 genomes]
rs12990732	0.82[EUR][1000 genomes]
rs13007109	0.85[EUR][1000 genomes]
rs13026575	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13033704	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13034739	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13035416	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13387187	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390258	0.90[ASN][1000 genomes]
rs13412585	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17343815	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17415725	0.85[EUR][1000 genomes]
rs35028480	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710809	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740698	0.98[ASN][1000 genomes]
rs7573223	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7573805	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578711	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7579041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593062	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605118	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9677271	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
2	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
3	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
4	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
5	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1004645	chr2:54686497-54718440	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1008888	chr2:54690695-54715300	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54685200-54694600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54685200-54696600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54685400-54696600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:54686400-54691400	Enhancers	Brain Substantia Nigra	brain
5	chr2:54686400-54694000	Weak transcription	Fetal Stomach	stomach
6	chr2:54686400-54695600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:54686400-54697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:54686600-54692200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:54686600-54692400	Weak transcription	Osteobl	bone
10	chr2:54686600-54694000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:54686600-54694000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:54686600-54695000	Enhancers	Fetal Heart	heart
13	chr2:54686600-54696200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:54686600-54696600	Weak transcription	Lung	lung
15	chr2:54686600-54696800	Weak transcription	NH-A	brain
16	chr2:54686600-54697000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:54686600-54698600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:54687000-54691000	Weak transcription	HUVEC	blood vessel
19	chr2:54687000-54691800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:54687000-54700800	Weak transcription	Brain Germinal Matrix	brain
21	chr2:54687200-54692400	Weak transcription	A549	lung
22	chr2:54687600-54692200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:54687600-54696800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:54688000-54691600	Enhancers	HepG2	liver
25	chr2:54688000-54692600	Enhancers	Adipose Nuclei	Adipose
26	chr2:54688400-54691600	Enhancers	Brain Anterior Caudate	brain
27	chr2:54688400-54694600	Enhancers	Colon Smooth Muscle	Colon
28	chr2:54688600-54691400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:54688600-54696200	Weak transcription	Right Ventricle	heart
30	chr2:54689200-54691800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:54689400-54693000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:54689400-54693800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:54689400-54694000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:54689400-54694000	Weak transcription	NHLF	lung
35	chr2:54689600-54693800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:54690200-54692400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:54690200-54692400	Weak transcription	HSMM	muscle
38	chr2:54690200-54694200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:54690400-54691400	Enhancers	Fetal Lung	lung
40	chr2:54690400-54691600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:54690400-54693800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:54690400-54694000	Weak transcription	HSMMtube	muscle
43	chr2:54690600-54692200	Weak transcription	NHDF-Ad	bronchial
44	chr2:54690600-54692400	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:54690600-54693800	Weak transcription	Brain Angular Gyrus	brain
46	chr2:54690600-54694200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:54690600-54695200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:54690600-54696600	Weak transcription	Spleen	Spleen
49	chr2:54690800-54691200	Enhancers	Stomach Smooth Muscle	stomach
50	chr2:54690800-54691800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links