Variant report

Variant	rs651244
Chromosome Location	chr21:41007498-41007499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40684766..40687078-chr21:41006043..41008701,2	MCF-7	breast:
2	chr21:40973024..40975835-chr21:41005421..41007852,2	MCF-7	breast:
3	chr21:41000981..41003548-chr21:41005728..41009282,3	MCF-7	breast:
4	chr21:41004133..41006069-chr21:41006515..41009780,3	K562	blood:
5	chr21:41005974..41008004-chr21:41008331..41010017,2	MCF-7	breast:
6	chr21:41006829..41008566-chr21:41050503..41052458,2	K562	blood:
7	chr21:41006012..41008630-chr21:41106556..41108420,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225330	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000255568	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs651029	0.90[EUR][1000 genomes]
rs666085	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs667432	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs856995	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv459260	chr21:41000353-41028197	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv587485	chr21:41000353-41028197	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs651244	IGSF5	cis	Thyroid	GTEx
rs651244	B3GALT5	cis	Thyroid	GTEx
rs651244	C21orf88	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40985600-41008400	Weak transcription	Pancreas	Pancrea
2	chr21:40990200-41008200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr21:40995800-41009000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr21:40998200-41014800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr21:40999400-41007800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr21:41002800-41008000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr21:41002800-41008200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:41002800-41013800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr21:41004400-41008200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr21:41005000-41008000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr21:41005000-41012000	Weak transcription	Small Intestine	intestine
12	chr21:41005200-41007800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr21:41005200-41008000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr21:41005200-41008000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr21:41005200-41008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr21:41005200-41008400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr21:41005400-41007800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr21:41005600-41008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr21:41006400-41007800	Weak transcription	Fetal Intestine Small	intestine
20	chr21:41006600-41007800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr21:41006600-41008200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:41006600-41008200	Weak transcription	Stomach Mucosa	stomach
23	chr21:41006600-41013000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr21:41006800-41007800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr21:41006800-41008200	Weak transcription	Fetal Intestine Large	intestine
26	chr21:41006800-41008400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr21:41006800-41008800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr21:41006800-41009600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr21:41006800-41010600	Weak transcription	Osteobl	bone
30	chr21:41007000-41008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:41007000-41008200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr21:41007000-41009200	Weak transcription	A549	lung
33	chr21:41007000-41009800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr21:41007200-41007600	Weak transcription	HSMMtube	muscle
35	chr21:41007200-41007800	Weak transcription	HSMM	muscle
36	chr21:41007200-41008200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr21:41007200-41010600	Weak transcription	NH-A	brain
38	chr21:41007400-41008800	Enhancers	Duodenum Mucosa	Duodenum

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