Variant report

Variant	rs671324
Chromosome Location	chr21:40984446-40984447
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs474656	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs512384	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs550569	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs651029	0.81[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs666085	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs667432	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs856995	0.82[CEU][hapmap];0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv11702	chr21:40981640-40987483	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv587484	chr21:40983133-40986120	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs671324	C21orf88	cis	Thyroid	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40970800-40984600	Weak transcription	Right Atrium	heart
2	chr21:40982800-40985200	Active TSS	Rectal Mucosa Donor 31	rectum
3	chr21:40982800-40986000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr21:40982800-40986400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr21:40983200-40984600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr21:40983200-40985600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr21:40983200-40987600	Active TSS	Brain Anterior Caudate	brain
8	chr21:40983400-40984600	Flanking Active TSS	NH-A	brain
9	chr21:40983400-40985200	Bivalent Enhancer	Fetal Brain Male	brain
10	chr21:40983400-40985600	Active TSS	Pancreas	Pancrea
11	chr21:40983400-40985800	Active TSS	Brain Hippocampus Middle	brain
12	chr21:40983400-40986200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr21:40983600-40984600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr21:40983600-40984800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr21:40983600-40985200	Active TSS	Brain Substantia Nigra	brain
16	chr21:40983600-40985800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:40983600-40986000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr21:40983600-40986000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
19	chr21:40983600-40986200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:40983600-40986600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
21	chr21:40983800-40985200	Enhancers	Fetal Heart	heart
22	chr21:40983800-40985600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr21:40984000-40984600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
24	chr21:40984000-40985200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr21:40984000-40985200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
26	chr21:40984000-40985400	Active TSS	Rectal Smooth Muscle	rectum
27	chr21:40984000-40985600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr21:40984000-40986200	Active TSS	H1 Cell Line	embryonic stem cell
29	chr21:40984200-40984600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr21:40984200-40984600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr21:40984200-40984600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr21:40984200-40984600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr21:40984200-40984600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr21:40984200-40984600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr21:40984200-40984600	Bivalent Enhancer	Left Ventricle	heart
36	chr21:40984200-40984600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr21:40984200-40984800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr21:40984200-40985200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr21:40984200-40985200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr21:40984200-40985200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
41	chr21:40984200-40985200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr21:40984200-40985200	Bivalent/Poised TSS	Fetal Brain Female	brain
43	chr21:40984200-40985600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr21:40984200-40985600	Active TSS	Colon Smooth Muscle	Colon
45	chr21:40984200-40985600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
46	chr21:40984200-40985600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
47	chr21:40984200-40985800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
48	chr21:40984200-40985800	Bivalent/Poised TSS	NHDF-Ad	bronchial
49	chr21:40984200-40986000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
50	chr21:40984200-40987400	Active TSS	Pancreatic Islets	Pancreatic Islet

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