Variant report

Variant	rs28759507
Chromosome Location	chr21:45208521-45208522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr21:45208402-45208660	GM12878	blood:	n/a	n/a
2	RPC155	chr21:45208096-45209406	K562	blood:	n/a	n/a
3	BCL3	chr21:45208383-45208673	GM12878	blood:	n/a	n/a
4	TAL1	chr21:45208353-45208691	K562	blood:	n/a	n/a
5	RPC155	chr21:45208468-45209102	Hela-S3	cervix:	n/a	n/a
6	TBP	chr21:45208299-45209794	K562	blood:	n/a	n/a
7	ZNF384	chr21:45208445-45209579	K562	blood:	n/a	n/a
8	PBX3	chr21:45208399-45208649	GM12878	blood:	n/a	n/a
9	JUN	chr21:45208373-45210623	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45158615..45161441-chr21:45207897..45210708,2	K562	blood:
2	chr21:45159250..45162021-chr21:45208113..45211544,3	MCF-7	breast:
3	chr21:45207900..45209521-chr21:45431429..45433903,2	MCF-7	breast:
4	chr21:45207339..45211369-chr21:45429720..45433341,4	K562	blood:
5	chr21:45136894..45141532-chr21:45205840..45211872,8	MCF-7	breast:
6	chr21:45130981..45133882-chr21:45206562..45209340,2	K562	blood:
7	chr21:45188049..45190841-chr21:45206908..45209310,2	MCF-7	breast:
8	chr21:45193334..45196312-chr21:45207752..45211007,4	MCF-7	breast:
9	chr21:45138000..45143848-chr21:45206375..45212489,9	MCF-7	breast:
10	chr21:45201612..45205256-chr21:45206995..45210818,5	MCF-7	breast:
11	chr21:45076259..45080839-chr21:45207005..45211007,4	MCF-7	breast:

No data

Variant related genes	Relation type
RRP1	TF binding region
ENSG00000160209	Chromatin interaction
ENSG00000160207	Chromatin interaction
ENSG00000160208	Chromatin interaction
ENSG00000234030	Chromatin interaction
ENSG00000160218	Chromatin interaction
ENSG00000160213	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11089097	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1136072	0.94[EUR][1000 genomes]
rs11909278	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1537118	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1537120	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17004612	0.81[JPT][hapmap]
rs2070538	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838364	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838367	0.85[ASW][hapmap];0.85[YRI][hapmap]
rs2838373	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838376	0.86[CHB][hapmap];0.82[MEX][hapmap]
rs2838379	0.86[CHB][hapmap]
rs2838380	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838385	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2838391	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838400	0.90[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs2838401	0.81[CHB][hapmap]
rs2838402	0.81[CHB][hapmap]
rs2838405	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2838414	0.81[CEU][hapmap]
rs28544397	0.87[AFR][1000 genomes]
rs34851196	0.81[EUR][1000 genomes]
rs4566449	0.86[CHB][hapmap];0.90[MEX][hapmap]
rs4819314	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[ASN][1000 genomes]
rs55663506	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55825369	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55830074	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs55889756	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs55982230	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56387943	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59406851	0.80[ASN][1000 genomes]
rs60418573	0.99[ASN][1000 genomes]
rs61028951	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62227538	0.82[EUR][1000 genomes]
rs62229234	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62230077	0.82[ASN][1000 genomes]
rs6518321	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67676705	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7276362	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7276547	0.90[EUR][1000 genomes]
rs8128323	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8132984	0.86[EUR][1000 genomes]
rs915770	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9808695	0.82[MEX][hapmap]
rs9976535	0.95[ASN][1000 genomes]
rs9979356	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs9980220	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9981458	0.86[AFR][1000 genomes]
rs9984420	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv913876	chr21:45119629-45267193	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2830066	chr21:45133868-45258047	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv913879	chr21:45145286-45237039	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv913880	chr21:45145286-45263920	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv913881	chr21:45145286-45267193	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv470904	chr21:45151045-45258047	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv834107	chr21:45155325-45294546	Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
11	nsv520305	chr21:45175958-45246326	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv913883	chr21:45191139-45252838	Weak transcription Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv913884	chr21:45191139-45255836	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv544469	chr21:45194085-45257959	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	esv3347263	chr21:45204424-45209222	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
17	nsv913885	chr21:45206355-45249474	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28759507	RSPH1	cis	cerebellum	SCAN
rs28759507	C21orf88	cis	parietal	SCAN
rs28759507	B3GALT5	cis	cerebellum	SCAN
rs28759507	CSTB	Cis_1M	lymphoblastoid	RTeQTL
rs28759507	TRAPPC10	cis	cerebellum	SCAN
rs28759507	MCM3APAS	cis	parietal	SCAN
rs28759507	C21orf2	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45196800-45208800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr21:45196800-45209000	Weak transcription	Aorta	Aorta
3	chr21:45199000-45208600	Weak transcription	Stomach Mucosa	stomach
4	chr21:45199000-45208800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:45199200-45208600	Weak transcription	Primary T cells from cord blood	blood
6	chr21:45199400-45208600	Weak transcription	Primary B cells from cord blood	blood
7	chr21:45202600-45208600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr21:45203200-45208800	Weak transcription	HMEC	breast
9	chr21:45203600-45208600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr21:45203600-45208600	Weak transcription	A549	lung
11	chr21:45203800-45208600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr21:45203800-45208600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr21:45203800-45208600	Weak transcription	Adipose Nuclei	Adipose
14	chr21:45203800-45208600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr21:45204600-45208600	Weak transcription	HepG2	liver
16	chr21:45204600-45208600	Weak transcription	NHEK	skin
17	chr21:45204600-45209000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr21:45204800-45208600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr21:45207000-45208800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr21:45207000-45208800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr21:45207200-45208600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr21:45207200-45208800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:45207200-45208800	Weak transcription	Colonic Mucosa	Colon
24	chr21:45207200-45209000	Weak transcription	Lung	lung
25	chr21:45207200-45209400	Weak transcription	Spleen	Spleen
26	chr21:45207400-45208800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr21:45207400-45208800	Weak transcription	Esophagus	oesophagus
28	chr21:45207400-45209000	Weak transcription	Gastric	stomach
29	chr21:45208400-45208600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr21:45208400-45208600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr21:45208400-45208600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr21:45208400-45208600	Enhancers	Primary B cells from peripheral blood	blood
33	chr21:45208400-45208600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr21:45208400-45208600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr21:45208400-45208600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr21:45208400-45208600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr21:45208400-45208600	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr21:45208400-45208600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr21:45208400-45208600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr21:45208400-45208600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr21:45208400-45208600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr21:45208400-45208600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr21:45208400-45208600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr21:45208400-45208600	Enhancers	Brain Germinal Matrix	brain
45	chr21:45208400-45208600	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr21:45208400-45208600	Enhancers	Fetal Brain Male	brain
47	chr21:45208400-45208600	Enhancers	Placenta	Placenta
48	chr21:45208400-45208600	Flanking Active TSS	GM12878-XiMat	blood
49	chr21:45208400-45208600	Enhancers	Hela-S3	cervix
50	chr21:45208400-45208600	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links