Variant report

Variant	rs2605242
Chromosome Location	chr4:48910970-48910971
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	chr4:48907689..48909984-chr4:48910157..48911988,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145247	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2243811	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2249306	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2354945	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2354946	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2572336	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2572346	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2572348	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2572349	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2605234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2605241	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2605269	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4695410	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4695411	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6447669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7654550	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7686885	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48909000-48911000	Weak transcription	NHDF-Ad	bronchial
2	chr4:48909000-48911000	Weak transcription	NHLF	lung
3	chr4:48909000-48911200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:48909000-48911200	Weak transcription	HSMM	muscle
5	chr4:48909000-48911200	Weak transcription	HSMMtube	muscle
6	chr4:48909000-48911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:48909200-48911000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:48909200-48911000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:48909200-48911000	Weak transcription	Osteobl	bone
10	chr4:48909200-48911200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:48909200-48911400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:48909200-48911400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:48909200-48911600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:48909200-48911600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:48909200-48911600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:48909200-48914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:48909200-48916200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:48909400-48911000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:48909400-48911000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:48909400-48911000	Weak transcription	Hela-S3	cervix
21	chr4:48909400-48911000	Weak transcription	HUVEC	blood vessel
22	chr4:48909400-48911200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:48909400-48911200	Weak transcription	A549	lung
24	chr4:48909400-48914600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:48909400-48917200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:48909600-48911800	Weak transcription	Primary T cells from cord blood	blood
27	chr4:48909800-48912000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:48910000-48911800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:48910000-48913400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:48910200-48911200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:48910200-48911800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr4:48910400-48913000	Enhancers	NHEK	skin
33	chr4:48910600-48914600	Weak transcription	Esophagus	oesophagus
34	chr4:48910800-48911200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:48910800-48911200	Weak transcription	Stomach Mucosa	stomach
36	chr4:48910800-48911800	Enhancers	NH-A	brain
37	chr4:48910800-48912200	Enhancers	HMEC	breast

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