Variant report

Variant	rs452875
Chromosome Location	chr5:9452016-9452017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1849363	0.88[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs268523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs268525	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs268527	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs268530	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs268531	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs396049	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs436243	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs623033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907655	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9437400-9477800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:9441600-9456200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:9442000-9454000	Weak transcription	Osteobl	bone
4	chr5:9445400-9453400	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:9448000-9453400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:9448600-9452600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:9448600-9453600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:9448600-9463800	Weak transcription	Fetal Stomach	stomach
9	chr5:9448600-9467000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:9449000-9452200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:9449000-9453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:9449000-9454200	Weak transcription	NHLF	lung
13	chr5:9449200-9452200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:9449600-9452200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:9449600-9453200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:9450000-9454400	Enhancers	Fetal Heart	heart
17	chr5:9450200-9453200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:9450400-9452400	Enhancers	Brain Substantia Nigra	brain
19	chr5:9450400-9452600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:9450600-9453200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:9450600-9454600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:9450800-9452200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:9451000-9453000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:9451200-9452600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:9451200-9452800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:9451200-9453000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:9451400-9452400	Enhancers	Brain Angular Gyrus	brain
28	chr5:9451400-9453000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:9451400-9453000	Enhancers	Brain Germinal Matrix	brain
30	chr5:9451600-9452600	Enhancers	Brain Cingulate Gyrus	brain
31	chr5:9451600-9452600	Enhancers	Brain Hippocampus Middle	brain
32	chr5:9451600-9455800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr5:9451800-9452200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:9451800-9452400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr5:9451800-9452600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:9451800-9452600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:9451800-9453000	Enhancers	Left Ventricle	heart
38	chr5:9451800-9454400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:9451800-9454600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:9451800-9455800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:9451800-9456200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr5:9451800-9458600	Weak transcription	Right Ventricle	heart
43	chr5:9452000-9452400	Enhancers	Brain Inferior Temporal Lobe	brain

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