Variant report

Variant	rs856995
Chromosome Location	chr21:41006225-41006226
allele	C/T
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	chr21:41004099..41006698-chr21:41012872..41015470,2	MCF-7	breast:
3	chr21:40973024..40975835-chr21:41005421..41007852,2	MCF-7	breast:
4	chr21:41000981..41003548-chr21:41005728..41009282,3	MCF-7	breast:
5	chr21:41005974..41008004-chr21:41008331..41010017,2	MCF-7	breast:
6	chr21:41006012..41008630-chr21:41106556..41108420,2	MCF-7	breast:

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

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs474656	0.89[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs512384	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs634486	0.90[JPT][hapmap]
rs651029	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs651244	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671324	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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs856995	IGSF5	cis	Thyroid	GTEx
rs856995	C21orf88	cis	Thyroid	GTEx

Chromatin state (count:48 , 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	chr21:41001200-41006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr21:41002000-41006600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr21:41002200-41006600	Enhancers	Stomach Mucosa	stomach
9	chr21:41002400-41007000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:41002800-41008000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr21:41002800-41008200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:41002800-41013800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr21:41004000-41006600	Enhancers	NHLF	lung
14	chr21:41004400-41008200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr21:41004600-41006800	Enhancers	NHDF-Ad	bronchial
16	chr21:41004600-41007000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr21:41004600-41007200	Enhancers	HSMM	muscle
18	chr21:41005000-41006600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr21:41005000-41008000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr21:41005000-41012000	Weak transcription	Small Intestine	intestine
21	chr21:41005200-41007800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr21:41005200-41008000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr21:41005200-41008000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr21:41005200-41008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr21:41005200-41008400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr21:41005400-41006400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr21:41005400-41006400	Enhancers	Fetal Intestine Small	intestine
28	chr21:41005400-41007800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr21:41005600-41008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr21:41005800-41006600	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr21:41005800-41006800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr21:41005800-41006800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr21:41005800-41006800	Enhancers	Fetal Intestine Large	intestine
34	chr21:41005800-41007200	Enhancers	NH-A	brain
35	chr21:41006000-41006400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr21:41006000-41006400	Flanking Active TSS	A549	lung
37	chr21:41006000-41006400	Flanking Active TSS	Osteobl	bone
38	chr21:41006000-41006600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr21:41006000-41006600	Flanking Active TSS	HSMMtube	muscle
40	chr21:41006000-41006800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr21:41006000-41006800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr21:41006000-41007000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr21:41006200-41006400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr21:41006200-41006600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:41006200-41006600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr21:41006200-41006800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr21:41006200-41006800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr21:41006200-41007000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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