Variant report

Variant	rs2035560
Chromosome Location	chr3:85010790-85010791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17022126	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1994316	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2200467	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4856556	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4856557	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55692107	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55804926	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55980308	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73137638	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73137655	0.91[AMR][1000 genomes]
rs73137667	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73137668	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73137671	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73137672	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73137679	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73139653	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73139656	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73139658	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73139660	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73139669	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73139677	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73139679	0.86[AMR][1000 genomes];0.81[EUR][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	esv3381298	chr3:84689266-85030314	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482371	chr3:84880813-85031486	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv471620	chr3:84880814-85031486	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1010140	chr3:84997012-85034281	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85007200-85011800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr3:85007200-85012400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:85007200-85012600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:85007400-85011200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:85007400-85011600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:85007400-85012000	Active TSS	Brain Cingulate Gyrus	brain
7	chr3:85007600-85011000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:85007600-85011200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:85007600-85012200	Active TSS	Brain Anterior Caudate	brain
10	chr3:85007800-85011200	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr3:85007800-85011400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:85007800-85011400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:85007800-85012000	Active TSS	Brain Hippocampus Middle	brain
14	chr3:85007800-85012200	Active TSS	Brain Substantia Nigra	brain
15	chr3:85007800-85012600	Active TSS	Brain Angular Gyrus	brain
16	chr3:85008600-85011000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr3:85008600-85011000	Bivalent Enhancer	Fetal Heart	heart
18	chr3:85008600-85011200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:85008800-85010800	Enhancers	Pancreas	Pancrea
20	chr3:85008800-85011000	Active TSS	Right Atrium	heart
21	chr3:85009200-85010800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:85009200-85011000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:85009200-85011200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:85009200-85011200	Active TSS	Psoas Muscle	Psoas
25	chr3:85009200-85011200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:85009400-85011000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:85009400-85011000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:85009400-85011200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr3:85009400-85012000	Active TSS	Brain Germinal Matrix	brain
30	chr3:85009600-85010800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:85009800-85011000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr3:85009800-85011000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr3:85009800-85011000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr3:85009800-85011200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:85010000-85010800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
36	chr3:85010000-85010800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
37	chr3:85010200-85011600	Active TSS	Fetal Brain Female	brain
38	chr3:85010400-85010800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
39	chr3:85010400-85011000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
40	chr3:85010400-85011000	Bivalent/Poised TSS	NH-A	brain
41	chr3:85010600-85010800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:85010600-85010800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:85010600-85010800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:85010600-85010800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:85010600-85010800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr3:85010600-85010800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
47	chr3:85010600-85010800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:85010600-85010800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
49	chr3:85010600-85010800	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr3:85010600-85011000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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