Variant report

Variant	rs1983009
Chromosome Location	chr3:98558048-98558049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:20354331..20356864-chr3:98555209..98558194,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10589669	0.82[EUR][1000 genomes]
rs12107272	0.82[EUR][1000 genomes]
rs12108018	0.84[EUR][1000 genomes]
rs13065136	0.82[EUR][1000 genomes]
rs13074614	0.84[EUR][1000 genomes]
rs13076960	0.84[EUR][1000 genomes]
rs13081992	0.82[EUR][1000 genomes]
rs13083238	0.84[EUR][1000 genomes]
rs13083934	0.84[EUR][1000 genomes]
rs13084692	0.84[EUR][1000 genomes]
rs13087627	0.82[EUR][1000 genomes]
rs13087631	0.84[EUR][1000 genomes]
rs13091170	0.82[EUR][1000 genomes]
rs13096085	0.82[EUR][1000 genomes]
rs13097876	0.82[EUR][1000 genomes]
rs13100915	0.82[EUR][1000 genomes]
rs13100937	0.82[EUR][1000 genomes]
rs34008360	0.84[EUR][1000 genomes]
rs34269725	0.82[EUR][1000 genomes]
rs34279227	0.84[EUR][1000 genomes]
rs34284740	0.82[EUR][1000 genomes]
rs34489202	0.82[EUR][1000 genomes]
rs34688367	0.84[EUR][1000 genomes]
rs34711372	0.84[EUR][1000 genomes]
rs34725039	0.82[EUR][1000 genomes]
rs34826460	0.82[EUR][1000 genomes]
rs34848749	0.84[EUR][1000 genomes]
rs34860591	0.82[EUR][1000 genomes]
rs35006699	0.84[EUR][1000 genomes]
rs35025156	0.82[EUR][1000 genomes]
rs35098355	0.84[EUR][1000 genomes]
rs35103318	0.82[EUR][1000 genomes]
rs35219252	0.84[EUR][1000 genomes]
rs35239055	0.84[EUR][1000 genomes]
rs35312318	0.82[EUR][1000 genomes]
rs35366262	0.84[EUR][1000 genomes]
rs35422064	0.84[EUR][1000 genomes]
rs35499232	0.82[EUR][1000 genomes]
rs35514544	0.82[EUR][1000 genomes]
rs35539438	0.82[EUR][1000 genomes]
rs35764973	0.82[EUR][1000 genomes]
rs35914268	0.84[EUR][1000 genomes]
rs35947806	0.84[EUR][1000 genomes]
rs36098932	0.82[EUR][1000 genomes]
rs36157152	0.82[EUR][1000 genomes]
rs55644421	0.84[EUR][1000 genomes]
rs56083233	0.82[EUR][1000 genomes]
rs56246599	0.82[EUR][1000 genomes]
rs6805362	0.84[EUR][1000 genomes]
rs71124004	0.86[EUR][1000 genomes]
rs71311398	0.84[EUR][1000 genomes]
rs71311402	0.84[EUR][1000 genomes]
rs71313504	0.82[EUR][1000 genomes]
rs71313508	0.82[EUR][1000 genomes]
rs71313509	0.82[EUR][1000 genomes]
rs71313510	0.82[EUR][1000 genomes]
rs71313511	0.82[EUR][1000 genomes]
rs7614053	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS 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
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	esv3325835	chr3:98556087-98558635	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:98536200-98594200	Weak transcription	HepG2	liver
5	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:98537000-98592800	Weak transcription	K562	blood
7	chr3:98538200-98569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:98541200-98567000	Weak transcription	Liver	Liver
9	chr3:98541400-98565000	Weak transcription	HUVEC	blood vessel
10	chr3:98545400-98561600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:98548800-98566600	Weak transcription	Adipose Nuclei	Adipose
12	chr3:98550200-98568600	Weak transcription	Thymus	Thymus
13	chr3:98550800-98561800	Weak transcription	HSMMtube	muscle
14	chr3:98551600-98562000	Weak transcription	Fetal Heart	heart
15	chr3:98552600-98566600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:98552600-98567000	Weak transcription	Fetal Kidney	kidney
17	chr3:98552800-98558200	Weak transcription	A549	lung
18	chr3:98552800-98561400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:98552800-98566600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:98552800-98575800	Weak transcription	Pancreas	Pancrea
21	chr3:98552800-98578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
23	chr3:98553000-98558200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:98553000-98558200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:98553000-98558200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:98553000-98558200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:98553000-98558200	Weak transcription	HSMM	muscle
28	chr3:98553000-98558200	Weak transcription	NHDF-Ad	bronchial
29	chr3:98553000-98558200	Weak transcription	Osteobl	bone
30	chr3:98553000-98558400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:98553000-98558600	Weak transcription	NHEK	skin
32	chr3:98553000-98558800	Weak transcription	HMEC	breast
33	chr3:98553000-98559200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:98553000-98559400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:98553000-98559400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:98553000-98561400	Weak transcription	Fetal Lung	lung
37	chr3:98553000-98562400	Weak transcription	NHLF	lung
38	chr3:98553000-98563200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:98553000-98565800	Weak transcription	Ovary	ovary
40	chr3:98553000-98566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:98553000-98566800	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:98553000-98567000	Weak transcription	Brain Germinal Matrix	brain
43	chr3:98553000-98575600	Weak transcription	Fetal Stomach	stomach
44	chr3:98553000-98576000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:98553000-98576200	Weak transcription	Left Ventricle	heart
46	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:98553200-98558200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:98553600-98558200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:98556600-98559600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:98556800-98558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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