Variant report

Variant	rs60040560
Chromosome Location	chr4:15697466-15697467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15697208..15699857-chr4:15706552..15708335,2	MCF-7	breast:
2	chr4:15697378..15700153-chr4:15707474..15709331,2	K562	blood:
3	chr4:15695760..15698048-chr4:15975957..15978418,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109743	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10003739	0.81[EUR][1000 genomes]
rs10008875	0.81[EUR][1000 genomes]
rs10008889	0.82[EUR][1000 genomes]
rs10017295	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10022610	0.82[EUR][1000 genomes]
rs10026851	0.81[EUR][1000 genomes]
rs10030313	0.81[EUR][1000 genomes]
rs10031017	0.82[EUR][1000 genomes]
rs10034328	0.81[EUR][1000 genomes]
rs10939628	0.81[EUR][1000 genomes]
rs11932730	0.81[EUR][1000 genomes]
rs11933521	0.81[EUR][1000 genomes]
rs11942335	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11943107	0.81[EUR][1000 genomes]
rs12503015	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12508186	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12511894	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12640192	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12645849	0.82[EUR][1000 genomes]
rs13116304	0.81[EUR][1000 genomes]
rs13121363	0.81[EUR][1000 genomes]
rs16892152	0.80[EUR][1000 genomes]
rs2041671	0.80[EUR][1000 genomes]
rs2160044	0.80[EUR][1000 genomes]
rs28534607	0.80[EUR][1000 genomes]
rs4235380	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4279203	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280723	0.81[EUR][1000 genomes]
rs4280724	0.81[EUR][1000 genomes]
rs4583752	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4591601	0.81[EUR][1000 genomes]
rs4642244	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4698403	0.82[EUR][1000 genomes]
rs4698405	0.81[EUR][1000 genomes]
rs4698408	0.82[EUR][1000 genomes]
rs62290605	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6449149	0.81[EUR][1000 genomes]
rs6839438	0.80[EUR][1000 genomes]
rs73125616	0.85[EUR][1000 genomes]
rs73125627	0.87[EUR][1000 genomes]
rs73125637	0.87[EUR][1000 genomes]
rs741180	0.81[EUR][1000 genomes]
rs7665390	0.81[EUR][1000 genomes]
rs7682586	0.82[EUR][1000 genomes]
rs872678	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15684000-15704400	Weak transcription	Left Ventricle	heart
2	chr4:15684800-15704400	Weak transcription	Aorta	Aorta
3	chr4:15686600-15704400	Weak transcription	Thymus	Thymus
4	chr4:15687200-15701200	Weak transcription	Fetal Intestine Small	intestine
5	chr4:15688400-15703800	Weak transcription	Fetal Kidney	kidney
6	chr4:15690600-15697800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:15691000-15698600	Weak transcription	Dnd41	blood
8	chr4:15691400-15698400	Weak transcription	Primary T cells from cord blood	blood
9	chr4:15691400-15698400	Weak transcription	Liver	Liver
10	chr4:15691400-15704000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:15691400-15704200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:15692200-15704000	Weak transcription	Brain Germinal Matrix	brain
13	chr4:15693200-15701600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:15693400-15702800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:15693600-15698800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr4:15693600-15701800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:15694200-15699000	Weak transcription	Primary B cells from cord blood	blood
18	chr4:15694800-15703800	Weak transcription	Brain Substantia Nigra	brain
19	chr4:15695400-15699400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr4:15695600-15697800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:15695600-15697800	Enhancers	NHEK	skin
22	chr4:15695800-15697600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:15695800-15697800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr4:15695800-15697800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:15695800-15697800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr4:15695800-15697800	Enhancers	HMEC	breast
27	chr4:15696000-15697600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr4:15696200-15697600	Flanking Active TSS	A549	lung
29	chr4:15696200-15697800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:15696200-15697800	Enhancers	HSMM	muscle
31	chr4:15696200-15698000	Enhancers	NHDF-Ad	bronchial
32	chr4:15696200-15698800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:15696400-15697600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:15696400-15697800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr4:15696400-15697800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:15696400-15697800	Enhancers	NHLF	lung
37	chr4:15696600-15697800	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr4:15696600-15698000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:15696600-15698000	Enhancers	Hela-S3	cervix
40	chr4:15696800-15697600	Enhancers	H1 Cell Line	embryonic stem cell
41	chr4:15696800-15697600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:15696800-15697600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr4:15696800-15697600	Enhancers	HUVEC	blood vessel
44	chr4:15697000-15697600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:15697000-15697600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:15697000-15697600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:15697000-15697600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr4:15697000-15697600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:15697000-15697600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:15697000-15697600	Enhancers	Esophagus	oesophagus

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