Variant report

Variant	rs4635562
Chromosome Location	chr2:54689829-54689830
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54682049..54684426-chr2:54689582..54692090,2	MCF-7	breast:
2	chr2:54682033..54684449-chr2:54688583..54690442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10171331	0.81[EUR][1000 genomes]
rs10205013	0.81[EUR][1000 genomes]
rs12477221	0.81[EUR][1000 genomes]
rs12617727	0.90[AFR][1000 genomes]
rs12621180	0.90[AFR][1000 genomes]
rs17039554	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045917	0.94[EUR][1000 genomes]
rs3087854	0.81[EUR][1000 genomes]
rs35001659	0.93[ASN][1000 genomes]
rs4233950	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4561702	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671218	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671933	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4671940	0.84[EUR][1000 genomes]
rs4671943	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56039013	0.90[AFR][1000 genomes]
rs56138820	0.90[AFR][1000 genomes]
rs57904903	0.90[AFR][1000 genomes]
rs59586067	0.90[AFR][1000 genomes]
rs6545409	0.81[EUR][1000 genomes]
rs6718276	0.81[EUR][1000 genomes]
rs6754429	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72618659	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72618660	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72618661	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72618662	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73932835	0.88[AFR][1000 genomes]
rs73932840	0.90[AFR][1000 genomes]
rs73932845	0.90[AFR][1000 genomes]
rs7599380	0.87[AMR][1000 genomes];0.96[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	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1004645	chr2:54686497-54718440	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54685200-54690200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:54685200-54690400	Weak transcription	Pancreas	Pancrea
3	chr2:54685200-54694600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:54685200-54696600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:54685400-54696600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:54686400-54691400	Enhancers	Brain Substantia Nigra	brain
7	chr2:54686400-54694000	Weak transcription	Fetal Stomach	stomach
8	chr2:54686400-54695600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:54686400-54697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:54686600-54690600	Enhancers	NHDF-Ad	bronchial
11	chr2:54686600-54692200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:54686600-54692400	Weak transcription	Osteobl	bone
13	chr2:54686600-54694000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:54686600-54694000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:54686600-54695000	Enhancers	Fetal Heart	heart
16	chr2:54686600-54696200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:54686600-54696600	Weak transcription	Lung	lung
18	chr2:54686600-54696800	Weak transcription	NH-A	brain
19	chr2:54686600-54697000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:54686600-54698600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:54686800-54690000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:54686800-54690600	Enhancers	Brain Angular Gyrus	brain
23	chr2:54687000-54690400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:54687000-54690600	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:54687000-54691000	Weak transcription	HUVEC	blood vessel
26	chr2:54687000-54691800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:54687000-54700800	Weak transcription	Brain Germinal Matrix	brain
28	chr2:54687200-54692400	Weak transcription	A549	lung
29	chr2:54687400-54690200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:54687600-54692200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:54687600-54696800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:54688000-54690200	Weak transcription	Spleen	Spleen
33	chr2:54688000-54690400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:54688000-54690600	Enhancers	Brain Hippocampus Middle	brain
35	chr2:54688000-54691600	Enhancers	HepG2	liver
36	chr2:54688000-54692600	Enhancers	Adipose Nuclei	Adipose
37	chr2:54688400-54690200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:54688400-54691600	Enhancers	Brain Anterior Caudate	brain
39	chr2:54688400-54694600	Enhancers	Colon Smooth Muscle	Colon
40	chr2:54688600-54691400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:54688600-54696200	Weak transcription	Right Ventricle	heart
42	chr2:54688800-54690200	Weak transcription	Fetal Brain Male	brain
43	chr2:54688800-54690200	Weak transcription	Psoas Muscle	Psoas
44	chr2:54688800-54690400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:54689000-54690200	Enhancers	HSMM	muscle
46	chr2:54689200-54690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:54689200-54690800	Enhancers	Fetal Brain Female	brain
48	chr2:54689200-54690800	Enhancers	Ovary	ovary
49	chr2:54689200-54691800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr2:54689400-54690200	Weak transcription	Brain Cingulate Gyrus	brain

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