Variant report

Variant	rs235284
Chromosome Location	chr21:46285665-46285666
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr21:46285542-46285682	GM12878	blood:	n/a	n/a
2	FOXP2	chr21:46285482-46285823	SK-N-MC	brain:	n/a	n/a
3	MAX	chr21:46285463-46286119	NB4	blood:	n/a	chr21:46285840-46285849
4	POLR2A	chr21:46285303-46286949	HepG2	liver:	n/a	n/a
5	SPI1	chr21:46285338-46286022	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:46285428-46286209	HL-60	blood:	n/a	n/a
7	EBF1	chr21:46285485-46285902	GM12878	blood:	n/a	n/a
8	RUNX3	chr21:46285453-46285932	GM12878	blood:	n/a	n/a
9	POLR2A	chr21:46285382-46286028	HL-60	blood:	n/a	n/a
10	MXI1	chr21:46285529-46285792	GM12878	blood:	n/a	n/a
11	SPI1	chr21:46285420-46285872	HL-60	blood:	n/a	n/a
12	SPI1	chr21:46285354-46286055	HL-60	blood:	n/a	n/a
13	SPI1	chr21:46285496-46285844	GM12891	blood:	n/a	n/a
14	MAX	chr21:46285011-46285886	MCF-7	breast:	n/a	chr21:46285293-46285304 chr21:46285294-46285304 chr21:46285294-46285303 chr21:46285295-46285302 chr21:46285840-46285849
15	EBF1	chr21:46285478-46285903	GM12878	blood:	n/a	n/a
16	BHLHE40	chr21:46285501-46285911	GM12878	blood:	n/a	n/a
17	SPI1	chr21:46285498-46285846	GM12878	blood:	n/a	n/a
18	SPI1	chr21:46285569-46285782	GM12878	blood:	n/a	n/a
19	RUNX3	chr21:46285467-46285822	GM12878	blood:	n/a	n/a
20	FOXA1	chr21:46285486-46285815	T-47D	breast:	n/a	n/a
21	EBF1	chr21:46285516-46285942	GM12878	blood:	n/a	n/a
22	POLR2A	chr21:46285329-46285841	HepG2	liver:	n/a	n/a
23	SPI1	chr21:46285488-46285889	GM12891	blood:	n/a	n/a
24	MYC	chr21:46285441-46285894	NB4	blood:	n/a	chr21:46285840-46285849
25	ZNF143	chr21:46285554-46285680	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46234824..46239565-chr21:46284858..46289652,5	K562	blood:
2	chr21:46236678..46239215-chr21:46284689..46286960,3	MCF-7	breast:

Variant related genes	Relation type
PTTG1IP	TF binding region
ENSG00000184900	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13050333	1.00[JPT][hapmap]
rs182893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs235259	0.84[GIH][hapmap]
rs2838715	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838718	0.92[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs689968	0.84[ASN][1000 genomes]
rs8126687	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription 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	51 gene(s)	inside rSNPs	diseases
3	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv913968	chr21:46249752-46301008	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv544479	chr21:46280467-46323401	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv470907	chr21:46283669-46306161	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv459299	chr21:46283669-46311264	Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	nsv459300	chr21:46283669-46311264	Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv587814	chr21:46283669-46311264	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs235284	KRTAP10-11	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46267400-46286600	Strong transcription	Fetal Stomach	stomach
2	chr21:46267600-46287000	Strong transcription	Brain Germinal Matrix	brain
3	chr21:46268200-46285800	Strong transcription	Fetal Muscle Leg	muscle
4	chr21:46268600-46285800	Strong transcription	Liver	Liver
5	chr21:46268600-46286000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr21:46268600-46286600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:46268800-46286600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:46268800-46286600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr21:46268800-46286600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr21:46269400-46285800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:46271400-46286800	Weak transcription	Psoas Muscle	Psoas
12	chr21:46273000-46286600	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr21:46275600-46290600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr21:46276400-46286000	Strong transcription	K562	blood
15	chr21:46277800-46286600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr21:46278200-46286400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr21:46278400-46289600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr21:46279400-46286600	Weak transcription	Fetal Brain Male	brain
19	chr21:46279400-46288400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr21:46279600-46288800	Weak transcription	Fetal Kidney	kidney
21	chr21:46279800-46287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr21:46281400-46286000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr21:46282000-46285800	Strong transcription	A549	lung
24	chr21:46282000-46286000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr21:46282200-46285800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr21:46282200-46286000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr21:46282200-46286200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr21:46283000-46286000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr21:46283400-46285800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr21:46283400-46285800	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr21:46283400-46286200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr21:46283400-46288800	Strong transcription	NHEK	skin
33	chr21:46283600-46285800	Strong transcription	Fetal Brain Female	brain
34	chr21:46283600-46286000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr21:46284000-46288400	Genic enhancers	Spleen	Spleen
36	chr21:46284000-46289000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr21:46284600-46287600	Genic enhancers	Fetal Intestine Large	intestine
38	chr21:46284600-46287800	Genic enhancers	Gastric	stomach
39	chr21:46284800-46286400	Genic enhancers	HSMM	muscle
40	chr21:46284800-46286600	Genic enhancers	HepG2	liver
41	chr21:46284800-46287200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr21:46284800-46287400	Genic enhancers	Placenta	Placenta
43	chr21:46284800-46288600	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr21:46285000-46287200	Genic enhancers	Rectal Mucosa Donor 29	rectum
45	chr21:46285000-46288400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr21:46285000-46291600	Enhancers	Primary hematopoietic stem cells	blood
47	chr21:46285000-46291800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr21:46285200-46285800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr21:46285200-46285800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr21:46285200-46285800	Genic enhancers	Brain Inferior Temporal Lobe	brain

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