Variant report

Variant	rs6545408
Chromosome Location	chr2:54697119-54697120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10200103	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10496032	0.90[ASN][1000 genomes]
rs12713259	0.89[ASN][1000 genomes]
rs4129261	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7566833	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7600596	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
8	nsv1008888	chr2:54690695-54715300	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3693290	chr2:54693204-54707562	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv438348	chr2:54693204-54714066	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv817939	chr2:54693204-54718181	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54686400-54697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:54686600-54698600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:54687000-54700800	Weak transcription	Brain Germinal Matrix	brain
4	chr2:54690800-54697600	Weak transcription	Fetal Brain Female	brain
5	chr2:54694400-54698800	Enhancers	Ovary	ovary
6	chr2:54695200-54701800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:54695400-54698400	Enhancers	Fetal Lung	lung
8	chr2:54695400-54698800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:54695600-54697800	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:54695600-54698200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr2:54695600-54698800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:54695600-54699000	Enhancers	Fetal Stomach	stomach
13	chr2:54695600-54699200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:54695600-54699800	Enhancers	Rectal Smooth Muscle	rectum
15	chr2:54695600-54699800	Enhancers	Osteobl	bone
16	chr2:54695600-54700200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:54695600-54700200	Enhancers	A549	lung
18	chr2:54695600-54701200	Enhancers	Brain Angular Gyrus	brain
19	chr2:54695600-54701400	Enhancers	Adipose Nuclei	Adipose
20	chr2:54695600-54701400	Enhancers	Brain Substantia Nigra	brain
21	chr2:54695600-54701800	Enhancers	Brain Anterior Caudate	brain
22	chr2:54695600-54701800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:54695800-54697400	Flanking Active TSS	HSMMtube	muscle
24	chr2:54695800-54697800	Enhancers	Stomach Smooth Muscle	stomach
25	chr2:54695800-54699000	Enhancers	Colon Smooth Muscle	Colon
26	chr2:54695800-54701600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:54696000-54697600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr2:54696000-54697600	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr2:54696000-54698000	Enhancers	Primary hematopoietic stem cells	blood
30	chr2:54696000-54698800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr2:54696000-54699200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:54696200-54697200	Enhancers	Placenta	Placenta
33	chr2:54696200-54698800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:54696200-54698800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:54696200-54699000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:54696200-54699000	Enhancers	Placenta Amnion	Placenta Amnion
37	chr2:54696200-54701200	Enhancers	Fetal Brain Male	brain
38	chr2:54696200-54701800	Enhancers	Brain Hippocampus Middle	brain
39	chr2:54696400-54697800	Genic enhancers	HepG2	liver
40	chr2:54696400-54698000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:54696400-54698400	Enhancers	GM12878-XiMat	blood
42	chr2:54696400-54699000	Enhancers	Psoas Muscle	Psoas
43	chr2:54696400-54699000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:54696400-54700000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:54696600-54697200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr2:54696600-54697200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:54696600-54697200	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr2:54696600-54697200	Flanking Active TSS	Right Atrium	heart
49	chr2:54696600-54698400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:54696600-54698600	Weak transcription	Pancreas	Pancrea

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