Variant report

Variant	rs9985035
Chromosome Location	chr21:45355492-45355493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45323009..45324981-chr21:45353834..45356371,2	K562	blood:
2	chr21:45330659..45332526-chr21:45353655..45356430,2	K562	blood:
3	chr21:45340527..45345737-chr21:45352879..45360873,10	K562	blood:
4	chr21:45283083..45285327-chr21:45354885..45356740,2	MCF-7	breast:
5	chr21:45281403..45288287-chr21:45354667..45363125,18	K562	blood:
6	chr21:45352880..45356983-chr21:45357815..45359696,3	MCF-7	breast:
7	chr21:45340582..45343200-chr21:45355048..45357219,2	MCF-7	breast:
8	chr21:45261344..45263558-chr21:45354374..45356683,2	K562	blood:
9	chr21:45233392..45235627-chr21:45355114..45357134,2	K562	blood:
10	chr21:45210542..45212642-chr21:45354588..45357125,2	K562	blood:
11	chr21:45347889..45351135-chr21:45352926..45356421,4	MCF-7	breast:
12	chr21:45354193..45356078-chr21:45363330..45365754,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1005192	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1573474	0.95[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs1888525	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070547	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838435	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838436	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838439	0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827246	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819340	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4819345	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4819348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518334	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs6518335	0.89[EUR][1000 genomes]
rs6518337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276578	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762411	0.86[JPT][hapmap]
rs762415	0.86[JPT][hapmap]
rs8127341	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs914196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9306164	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306165	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306166	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974282	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9978688	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv913888	chr21:45351206-45428278	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1055772	chr21:45353436-45373304	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9985035	TFF2	cis	cerebellum	SCAN
rs9985035	CSTB	cis	lymphoblastoid	seeQTL
rs9985035	POFUT2	cis	parietal	SCAN
rs9985035	RAB6A	trans	cerebellum	SCAN
rs9985035	ZNF295	cis	parietal	SCAN
rs9985035	ETS2	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45337600-45358600	Weak transcription	Osteobl	bone
2	chr21:45338800-45358600	Weak transcription	Hela-S3	cervix
3	chr21:45340800-45358800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr21:45341400-45358600	Weak transcription	A549	lung
5	chr21:45342200-45357000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:45342200-45358800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:45342400-45356400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr21:45343000-45357600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr21:45343000-45372400	Weak transcription	Small Intestine	intestine
10	chr21:45343400-45355600	Weak transcription	Brain Angular Gyrus	brain
11	chr21:45343600-45358000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr21:45343800-45356000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr21:45343800-45356200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr21:45343800-45357600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr21:45343800-45358600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr21:45343800-45358600	Weak transcription	HSMM	muscle
17	chr21:45343800-45358800	Weak transcription	Ovary	ovary
18	chr21:45343800-45379800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr21:45344000-45357200	Strong transcription	Fetal Stomach	stomach
20	chr21:45344400-45358400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr21:45345200-45358600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr21:45345400-45358600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:45348400-45356000	Weak transcription	Right Atrium	heart
24	chr21:45348400-45363800	Weak transcription	Aorta	Aorta
25	chr21:45348800-45356600	Weak transcription	Colon Smooth Muscle	Colon
26	chr21:45348800-45358600	Weak transcription	NHEK	skin
27	chr21:45349400-45355600	Strong transcription	Fetal Intestine Large	intestine
28	chr21:45349400-45357000	Strong transcription	Fetal Intestine Small	intestine
29	chr21:45349400-45359200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr21:45349800-45357600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr21:45350000-45357600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr21:45350000-45358400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr21:45350200-45355600	Weak transcription	HepG2	liver
34	chr21:45350200-45355800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr21:45350200-45357200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr21:45350200-45358600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr21:45350400-45355600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr21:45350400-45364000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr21:45350800-45355600	Weak transcription	Psoas Muscle	Psoas
40	chr21:45350800-45357600	Weak transcription	Primary B cells from cord blood	blood
41	chr21:45351000-45358400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr21:45351200-45358600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr21:45351200-45358600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr21:45351200-45358600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr21:45351600-45357000	Weak transcription	Fetal Thymus	thymus
46	chr21:45351800-45356400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr21:45352000-45355600	Strong transcription	NHLF	lung
48	chr21:45352000-45356800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr21:45352200-45356000	Weak transcription	Fetal Brain Male	brain
50	chr21:45352400-45368000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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