Variant report

Variant	rs10821447
Chromosome Location	chr9:97845505-97845506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:97845442-97845712	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr9:97845358-97846167	A549	lung:	n/a	n/a
3	POLR2A	chr9:97844992-97846197	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:97844233-97846110	Hela-S3	cervix:	n/a	n/a
5	BCL3	chr9:97845425-97846063	A549	lung:	n/a	n/a
6	POLR2A	chr9:97845353-97846140	A549	lung:	n/a	n/a
7	POLR2A	chr9:97845408-97846112	A549	lung:	n/a	n/a
8	POLR2A	chr9:97845207-97845548	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr9:97845419-97845791	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr9:97845479-97846022	HepG2	liver:	n/a	n/a
11	NR2C2	chr9:97845484-97846048	GM12878	blood:	n/a	n/a
12	POLR2A	chr9:97845410-97846111	A549	lung:	n/a	n/a
13	SIN3AK20	chr9:97845401-97845787	A549	lung:	n/a	n/a
14	POLR2A	chr9:97845057-97846135	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr9:97845326-97846172	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr9:97845461-97845747	HepG2	liver:	n/a	n/a
17	MAZ	chr9:97845503-97845648	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr9:97836122-97846291	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97840496..97842438-chr9:97844995..97846708,2	MCF-7	breast:
2	chr9:97844149..97846722-chr9:97853802..97855942,2	K562	blood:
3	chr9:97845277..97847054-chr9:97867436..97869989,2	K562	blood:

No data

Variant related genes	Relation type
MIR23B	TF binding region
MIR27B	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1011784	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739992	0.91[JPT][hapmap];0.91[LWK][hapmap]
rs10761374	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821451	0.80[ASN][1000 genomes]
rs10821455	0.91[JPT][hapmap]
rs1979022	0.91[JPT][hapmap]
rs2166402	0.91[JPT][hapmap];0.91[LWK][hapmap]
rs2297596	0.91[JPT][hapmap]
rs2297597	0.91[JPT][hapmap]
rs3277	0.91[JPT][hapmap]
rs3737142	0.91[JPT][hapmap]
rs3780564	0.91[JPT][hapmap]
rs3780568	0.91[JPT][hapmap];0.89[LWK][hapmap];0.83[YRI][hapmap]
rs3844341	0.91[JPT][hapmap]
rs3852402	0.91[JPT][hapmap]
rs4647459	0.91[JPT][hapmap]
rs4647462	0.91[JPT][hapmap]
rs4647475	0.91[JPT][hapmap]
rs4647528	0.91[JPT][hapmap];0.89[LWK][hapmap];0.83[YRI][hapmap]
rs4647554	0.91[JPT][hapmap];0.96[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4647558	0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4657	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743988	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744442	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744446	0.91[JPT][hapmap]
rs6479598	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7033633	0.83[TSI][hapmap]
rs7034538	0.91[JPT][hapmap]
rs7042293	0.87[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7042320	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7046682	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7850958	0.91[JPT][hapmap]
rs7854570	0.91[JPT][hapmap]
rs7874388	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963774	0.91[JPT][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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
6	esv3341854	chr9:97843531-97848029	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	266 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10821447	TDRD7	cis	cerebellum	SCAN
rs10821447	NINJ1	cis	cerebellum	SCAN
rs10821447	AUH	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
3	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:97826200-97847400	Weak transcription	HUVEC	blood vessel
7	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr9:97839200-97845800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:97839600-97845800	Genic enhancers	HSMM	muscle
10	chr9:97839600-97850400	Strong transcription	HepG2	liver
11	chr9:97839600-97851000	Genic enhancers	A549	lung
12	chr9:97840000-97850000	Strong transcription	Osteobl	bone
13	chr9:97840200-97846000	Genic enhancers	Left Ventricle	heart
14	chr9:97840800-97851800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr9:97841200-97845600	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:97841200-97846200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:97841200-97849800	Strong transcription	NH-A	brain
18	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:97841400-97853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:97841600-97847000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:97841600-97849200	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr9:97841600-97850000	Strong transcription	NHLF	lung
23	chr9:97841600-97855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:97841800-97851600	Strong transcription	Fetal Intestine Small	intestine
25	chr9:97841800-97853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:97841800-97854000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr9:97842200-97847200	Weak transcription	Dnd41	blood
28	chr9:97842200-97847600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:97842200-97848200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:97842200-97849600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:97842200-97850600	Strong transcription	Fetal Lung	lung
32	chr9:97842200-97852000	Strong transcription	NHEK	skin
33	chr9:97842400-97850000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:97842400-97850200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:97842400-97852600	Strong transcription	Fetal Intestine Large	intestine
36	chr9:97842400-97854200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr9:97842600-97845600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
38	chr9:97842800-97846000	Genic enhancers	Right Ventricle	heart
39	chr9:97842800-97846200	Genic enhancers	Esophagus	oesophagus
40	chr9:97842800-97846800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:97842800-97849400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:97842800-97849400	Strong transcription	NHDF-Ad	bronchial
43	chr9:97842800-97849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr9:97842800-97850800	Strong transcription	Placenta	Placenta
45	chr9:97843000-97846000	Strong transcription	Fetal Kidney	kidney
46	chr9:97843000-97846000	Genic enhancers	Pancreas	Pancrea
47	chr9:97843000-97846200	Genic enhancers	Colon Smooth Muscle	Colon
48	chr9:97843000-97846200	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr9:97843000-97846200	Strong transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:97843000-97846800	Genic enhancers	Brain Inferior Temporal Lobe	brain

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