Variant report

Variant	rs60697948
Chromosome Location	chr3:119895604-119895605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119810057..119817149-chr3:119894256..119903865,22	MCF-7	breast:
2	chr3:119809943..119817218-chr3:119893934..119905581,30	MCF-7	breast:
3	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13317366	0.88[AFR][1000 genomes]
rs16830754	0.87[AFR][1000 genomes]
rs2087749	0.87[AFR][1000 genomes]
rs28479821	1.00[AFR][1000 genomes]
rs9816977	0.88[AFR][1000 genomes]
rs9825665	0.88[AFR][1000 genomes]
rs9825897	1.00[AFR][1000 genomes]
rs9863105	0.88[AFR][1000 genomes]
rs9868903	0.87[AFR][1000 genomes]
rs9871988	1.00[AFR][1000 genomes]
rs9879732	0.88[AFR][1000 genomes]
rs9881856	0.88[AFR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	esv3403309	chr3:119892062-119896360	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv3342997	chr3:119892887-119895635	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
12	nsv513068	chr3:119893013-119895729	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
13	nsv518052	chr3:119893257-119896657	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119883200-119895800	Weak transcription	Fetal Intestine Small	intestine
3	chr3:119885000-119895800	Weak transcription	Fetal Lung	lung
4	chr3:119887200-119895800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:119888400-119895800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:119888400-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:119888400-119896200	Enhancers	NHDF-Ad	bronchial
8	chr3:119888600-119896000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:119890000-119895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:119890400-119895800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:119890400-119895800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:119890600-119895800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:119890800-119896000	Weak transcription	Right Atrium	heart
14	chr3:119891000-119895800	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:119891400-119896200	Weak transcription	Lung	lung
16	chr3:119892000-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:119892200-119895800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:119892200-119896000	Weak transcription	Fetal Stomach	stomach
19	chr3:119892400-119914200	Weak transcription	Fetal Brain Female	brain
20	chr3:119892800-119895800	Weak transcription	HSMM	muscle
21	chr3:119892800-119895800	Weak transcription	HSMMtube	muscle
22	chr3:119892800-119896200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:119893200-119896400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:119893400-119896200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:119893600-119896000	Enhancers	Osteobl	bone
26	chr3:119893600-119896200	Weak transcription	Aorta	Aorta
27	chr3:119893600-119897400	Enhancers	Placenta	Placenta
28	chr3:119894600-119896000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:119894600-119896000	Enhancers	HUVEC	blood vessel
30	chr3:119894800-119895800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:119894800-119895800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:119895000-119896000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:119895000-119896000	Weak transcription	Esophagus	oesophagus
34	chr3:119895200-119896200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:119895200-119897200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:119895400-119896200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:119895400-119896200	Enhancers	HMEC	breast
38	chr3:119895400-119897000	Enhancers	Psoas Muscle	Psoas
39	chr3:119895400-119897200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:119895600-119896000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:119895600-119896000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:119895600-119896000	Enhancers	Adipose Nuclei	Adipose
43	chr3:119895600-119896000	Enhancers	HepG2	liver
44	chr3:119895600-119896000	Enhancers	NHEK	skin
45	chr3:119895600-119896200	Enhancers	NHLF	lung
46	chr3:119895600-119896400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr3:119895600-119896800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:119895600-119897000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr3:119895600-119897000	Enhancers	Fetal Muscle Leg	muscle
50	chr3:119895600-119897000	Enhancers	Right Ventricle	heart

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